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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> |
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<html> |
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<head> |
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<title>Selection syntax for OOPSE utility programs</title> |
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</head> |
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<body style="background-color: white;"> |
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<basefont size="3"> |
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<div align="center"> |
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<p><font size="+2"><b>Selection syntax for OOPSE utility programs</b></font><span |
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style="font-weight: bold;"></span><br> |
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</p> |
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<h2 align="left"><a name="introduction" id="introduction"> Introduction |
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</a></h2> |
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<p style="text-align: left;">The OOPSE utility programs compute |
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properties from the <span |
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style="font-family: monospace; font-weight: bold;">dump</span><span |
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style="font-weight: bold;"> |
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</span>files that are generated during a molecular dynamics |
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simulation. |
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These programs are:<br> |
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</p> |
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<ul style="text-align: left;"> |
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<li><span style="font-family: monospace; font-weight: bold;">Dump2XYZ</span><span |
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style="font-weight: bold;"> </span>- Converts an OOPSE dump file into |
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a file suitable |
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for viewing in a molecular dynamics viewer like <a |
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href="http://www.jmol.org">Jmol</a><br> |
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</li> |
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<li><span style="font-family: monospace; font-weight: bold;">StaticProps</span><span |
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style="font-weight: bold;"> </span>- Computes static properties like |
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the pair distribution function, <span style="font-style: italic;">g(r)</span>.<br> |
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</li> |
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<li><span style="font-family: monospace; font-weight: bold;">DynamicProps</span><span |
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style="font-weight: bold;"> </span>- Computes time correlation |
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functions like the |
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velocity autocorrelation function, <span style="font-style: italic;"><<span |
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style="font-weight: bold;">v</span>(t)<span style="font-weight: bold;">v</span>(0)></span>, |
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or the mean square displacement <span style="font-style: italic;"><|<span |
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style="font-weight: bold;">r</span>(t) - <span |
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style="font-weight: bold;">r</span>(0)|<sup>2</sup>>.</span></li> |
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</ul> |
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<div style="text-align: left;">These programs often need to operate on |
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a subset of the data contained within a dump file. For example, |
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if you want only the <span style="font-style: italic;">oxygen-oxygen</span> |
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pair distribution from a water simulation, or if you want to make a |
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movie including only the water molecules within a 6 angstrom radius of |
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lipid head groups, you need a way to specify your selection to these |
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utility programs. OOPSE has a selection syntax which allows |
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you to specify the selection in a compact form in order to generate |
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only the data you want. For example a common use of the |
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StaticProps command would be:<br> |
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<br> |
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<div style="margin-left: 80px;"><span |
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style="font-family: monospace; font-weight: bold;">StaticProps -i |
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tp4.dump --gofr --sele1="select O*" --sele2="select O*"</span><br> |
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</div> |
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<br> |
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This command computes the oxygen-oxygen pair distribution function, <span |
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style="font-style: italic;">g<sub>OO</sub>(r)</span>, from a file |
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named <span style="font-family: monospace;">tp4.dump</span>. In |
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order to understand this selection syntax and to make full use of the |
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selection capabilities of the analysis programs, it is necessary to |
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understand a few of the core concepts that are used to perform |
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simulations.<br> |
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<h2><a name="Concepts"></a>Concepts</h2> |
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OOPSE manipulates both traditional atoms as well as some objects that <span |
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style="font-style: italic;">behave like atoms</span>. These |
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objects can be rigid collections of atoms or atoms which have |
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orientational degrees of freedom. Here is a diagram of the class |
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heirarchy:<br> |
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<span style="font-style: italic;"></span></div> |
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<p align="center"><img src="classoopse_1_1StuntDouble.png" height="136" |
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width="292"><br> |
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</p> |
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<ul style="text-align: left;"> |
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<li>A <span style="font-family: monospace; font-weight: bold;">StuntDouble</span> |
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is <span style="font-style: italic;">any</span> object that can be |
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manipulated by the integrators and minimizers.</li> |
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<li>An <span style="font-family: monospace; font-weight: bold;">Atom</span> |
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is a fundamental point-particle that can be moved around during a |
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simulation.</li> |
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<li>A <span style="font-family: monospace; font-weight: bold;">DirectionalAtom</span> |
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is an atom which has <span style="font-style: italic;">orientational</span> |
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as well as translational degrees of freedom.</li> |
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<li>A <span style="font-family: monospace; font-weight: bold;">RigidBody</span> |
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is a collection of <span |
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style="font-family: monospace; font-weight: bold;">Atom</span>s or <span |
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style="font-family: monospace; font-weight: bold;">DirectionalAtom</span>s |
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which behaves as a <span style="font-style: italic;">single unit.</span></li> |
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</ul> |
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<p align="left"> Every Molecule, Atom and DirectionalAtom in OOPSE |
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have their own names which are specified in the <span |
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style="font-family: monospace; font-weight: bold;">.md</span> file. In |
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contrast, RigidBodies are denoted by their membership and index inside |
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a particular molecule: <span style="font-family: monospace;">[MoleculeName]_RB_[index]</span> |
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(the contents inside |
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the brackets depend on the specifics of the simulation). The names of |
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rigid bodies are generated automatically. For |
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example, the name of the first rigid body in a DMPC molecule is |
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DMPC_RB_0.<br> |
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</p> |
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</div> |
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<h2><a name="select"></a>Syntax of the Select Command</h2> |
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The most general form of the select command is: <b>select <i>expression</i> |
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</b> |
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<p>This expression represents an arbitrary set of StuntDoubles (Atoms |
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or |
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RigidBodies) in OOPSE. Expressions are composed of either name |
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expressions, index expression, predefined sets, user-defined |
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expression, |
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comparison operators, within expressions, or logical combinations of |
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the above expression types. Expression can be combined using |
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parentheses |
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and the Boolean operators</p> |
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<p><b><a name="logic"></a> Logical expression. </b> </p> |
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<p>The logical operators allow complex queries to be constructed out of |
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simpler ones using the standard boolean connectives <b>and, or, not</b>. |
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Parentheses can be used to alter the precedence of the operators. |
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</p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="441"> |
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<tbody> |
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<tr bgcolor="#ffccff"> |
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<td width="174"> |
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<div align="left">logical operator </div> |
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</td> |
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<td width="241"> |
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<div align="left">equivalent operator</div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">and</div> |
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</td> |
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<td> |
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<div align="left">"&", "&&" </div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">or</div> |
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</td> |
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<td> |
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<div align="left">"|", "||", "," </div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">not</div> |
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</td> |
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<td> |
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<div align="left">"!"</div> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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<p> </p> |
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</ul> |
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<p><a name="name"><b> Name expression. |
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</b></a> </p> |
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<ul> |
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<table bgcolor="#ffffcc" border="1" bordercolor="#6b7683" width="886"> |
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<tbody> |
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<tr> |
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<td colspan="2"> |
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<div align="center">expression</div> |
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</td> |
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<td width="434"> |
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<div align="center">description</div> |
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</td> |
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</tr> |
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<tr> |
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<td rowspan="3" width="183">expression without "." </td> |
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<td width="247"> |
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<div align="left">select DMPC</div> |
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</td> |
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<td>select all StuntDoubles belonging to all DMPC molecules </td> |
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</tr> |
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<tr> |
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<td> |
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<div align="left">select C*</div> |
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</td> |
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<td>select all atoms which have atom types beginning with C<br> |
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</td> |
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</tr> |
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<tr> |
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<td> |
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<div align="left">select DMPC_RB_*</div> |
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</td> |
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<td>select all RigidBodies in DMPC molecules (only select |
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rigid-bodies, but not |
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include the atoms belong to them)</td> |
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</tr> |
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<tr> |
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<td rowspan="3">expression has one "." </td> |
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<td>select TIP3P.O_TIP3P</td> |
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<td>select the O_TIP3P Atoms belong to TIP3P molecules </td> |
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</tr> |
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<tr> |
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<td>select DMPC_RB_0.PO4</td> |
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<td>select the PO4 Atoms belonging to first RigidBody in each |
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DMPC molecule<br> |
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</td> |
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</tr> |
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<tr> |
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<td>select DMPC.20</td> |
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<td>select the 20th StuntDouble in each DMPC molecule<br> |
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</td> |
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</tr> |
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<tr> |
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<td>expression has two "."</td> |
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<td>select DMPC.DMPC_RB_?.*</td> |
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<td>select all Atoms belonging to all rigid-bodies within all |
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DMPC molecules</td> |
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</tr> |
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</tbody> |
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</table> |
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<p> </p> |
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</ul> |
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<p><a name="index" id="index"><b> Index expression </b></a></p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="894"> |
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<tbody> |
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<tr bgcolor="#ffffcc"> |
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<td width="113">select 20 </td> |
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<td width="520">select all of the StuntDoubles belonging to |
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Molecule 20</td> |
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</tr> |
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<tr bgcolor="#ffffcc"> |
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<td>select 20 to 30 </td> |
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<td>select all of the StuntDoules belonging to molecules which |
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have global |
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indices between 20 (inclusive) and 30 (exclusive) </td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> </p> |
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<p><a name="predefine" id="predefine"><b> Predefined sets </b></a></p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="449"> |
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<tbody> |
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<tr bgcolor="#ffccff"> |
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<td width="91"> |
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<div align="left">keyword</div> |
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</td> |
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<td width="332"> |
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<div align="left">description</div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">all</div> |
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</td> |
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<td> |
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<div align="left">select all StuntDoubles</div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">none</div> |
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</td> |
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<td> |
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<div align="left">select none of the StuntDoubles </div> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> </p> |
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<p><a name="user" id="user"><b> User defined expressions</b></a></p> |
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<p> Users can define arbitrary terms to represent groups of |
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StuntDoubles, and then use the define terms in select |
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commands. The general form for the define command is: <strong>define <em>term |
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expression</em></strong></p> |
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<p> Once defined, the user can specify such terms in boolean |
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expressions </p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="659"> |
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<tbody> |
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<tr bgcolor="#ffffcc"> |
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<td> |
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<p>define SSDWATER SSD or SSD1 or SSDRF</p> |
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<p>select SSDWATER </p> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p><a name="comparison" id="comparison"> <b>Comparison expression.</b></a></p> |
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<p>StuntDoubles can be selected by using comparision operators on |
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their properties. The general form for the comparison command is: a |
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property name, followed by a comparision operator and then a number.</p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="668"> |
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<tbody> |
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<tr bgcolor="#ffccff"> |
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<td width="305"> |
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<div align="left">property</div> |
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</td> |
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<td width="331"> |
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<div align="left">mass, dipole, charge </div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">comparision operator</div> |
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</td> |
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<td> |
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<div align="left">">", "<", "=", ">=", "<=", "!=" </div> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="672"> |
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<tbody> |
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<tr bgcolor="#ffffcc"> |
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<td width="302">select mass > 16.0 and charge < -2 </td> |
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<td width="338">select StuntDoubles which have mass greater |
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than |
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16.0 and charges less than -2 </td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> </p> |
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<p><b> <a name="within"></a> Within expression.</b> |
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</p> |
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<p> The "within" selection allows the user to select all StuntDoubles |
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within the specified |
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distance (in Angstroms) from a selection, including the selected atom |
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itself. The |
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general form for within selection is: <b>select within(<i>distance, |
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expression</i>) </b> |
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</p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="681"> |
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<tbody> |
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<tr bgcolor="#ffffcc"> |
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<td width="306">select within(2.5, PO4 or NC4) </td> |
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<td width="343"> |
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<blockquote>select all StuntDoubles which are within 2.5 |
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angstroms of PO4 or NC4 atoms<br> |
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</blockquote> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> |
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</p> |
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<h2><a name="syntax" id="syntax"> Tools which use the selection command |
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</a></h2> |
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<p><b><a name="within"></a> Dump2XYZ</b> |
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</p> |
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<p>Dump2XYZ can transform an OOPSE dump file into a xyz file which |
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could be opened by other molecular viewers, such as Jmol and VMD. </p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="890"> |
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<tbody> |
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<tr bgcolor="#6699ff"> |
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<td width="191"> |
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<blockquote> |
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<p>--selection</p> |
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</blockquote> |
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</td> |
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<td width="667">Specifying --selection="selection command" with |
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Dump2XYZ, user can select an arbitrary set of stuntdoubles to be |
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converted. </td> |
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</tr> |
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<tr bgcolor="#ccff99"> |
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<td> |
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<blockquote> |
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<p>--originsele</p> |
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</blockquote> |
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</td> |
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<td rowspan="2">In order to rotate the system, --originsele and |
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--refselec must be given to define the new coordinate set. A |
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stuntdouble with a dipole, which direction is always (0, 0, 1) in body |
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frame, is specified by --originsele. The new x-z plane is defined by |
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the direction of dipole and the StuntDouble is specified by --refsele. </td> |
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< |
</tr> |
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< |
<tr bgcolor="#ccff99"> |
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< |
<td> |
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< |
<blockquote> |
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<p>--refsele</p> |
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</blockquote> |
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</td> |
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< |
</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> |
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</p> |
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<p><b><a name="within"></a> StaticProps<br> |
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</b></p> |
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< |
StaticProps can compute properties which are averaged over the |
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< |
configurations that are contained within a dump file. The |
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< |
most common example of a static property that can be computed is the |
| 402 |
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pair distribution function between atoms of type A and other atoms of |
| 403 |
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type B, <span style="font-style: italic;">g<sub>AB</sub>(r)</span>. |
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StaticProps can also be used to compute the density distributions of |
| 405 |
< |
other molecules in a reference frame <span style="font-style: italic;">fixed |
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to the body-fixed reference frame</span> of a selected atom or rigid |
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body.<b><br> |
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</b> |
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<p> </p> |
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<p align="center"><img src="definition.jpg" height="540" width="720"></p> |
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<p align="left">There are five seperate radial distribution functions |
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availiable in OOPSE. Since every radial distrbution function invlove |
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the calculation between a pair, --sele1 and --sele2 must be given. |
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</p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="890"> |
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<tbody> |
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<tr bgcolor="#ccffcc"> |
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<td width="191"> |
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<blockquote> |
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<p>option</p> |
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</blockquote> |
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</td> |
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<td width="667"> |
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< |
<blockquote> |
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< |
<div align="center">description</div> |
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</blockquote> |
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</td> |
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< |
</tr> |
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< |
<tr bgcolor="#ccffcc"> |
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<td> |
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<blockquote> |
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<p>--gofr</p> |
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</blockquote> |
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< |
</td> |
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<td>Computes the pair distribution function.</td> |
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</tr> |
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<tr bgcolor="#ccffcc"> |
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< |
<td> |
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<blockquote> |
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<p>--r_theta</p> |
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</blockquote> |
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</td> |
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<td>Computes the angle-dependent pair distribution function. |
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The |
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angle is defined by the intermolecular vector r and z-axis of |
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DirectionalAtom A.<br> |
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</td> |
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< |
</tr> |
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<tr bgcolor="#ccffcc"> |
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<td> |
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<blockquote> |
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<p>--r_omega</p> |
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</blockquote> |
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</td> |
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<td>Computes an angle-dependent pair distribution function. The |
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angle is defined by the z-axes of the two DirectionalAtoms A and B.<br> |
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</td> |
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</tr> |
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<tr bgcolor="#ccffcc"> |
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< |
<td> |
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< |
<blockquote> |
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<p>--theta_omega</p> |
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</blockquote> |
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</td> |
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<td>Calculate the pair distribution of the two angles.</td> |
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< |
</tr> |
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< |
<tr bgcolor="#ccffcc"> |
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<td> |
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<blockquote> |
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<p>--gxyz</p> |
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</blockquote> |
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</td> |
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<td>Calculate the density distribution of particles |
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of type B in the body frame of particle A. Therefore, --originsele and |
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--refsele must be given to define A's internal coordinate set. </td> |
| 477 |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> </p> |
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<p><b><a name="within"></a> DynamicProps<br> |
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<span style="font-weight: bold;"><br> |
| 484 |
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</span></b>DynamicProps computes time correlation functions from the |
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< |
configurations stored in a dump file. Typical examples of time |
| 486 |
< |
correlation functions are the mean square displacement and the velocity |
| 487 |
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autocorrelation functions. <b><span style="font-weight: bold;"><br> |
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</span> </b></p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="890"> |
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<tbody> |
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< |
<tr bgcolor="#ccffcc"> |
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< |
<td width="191"> |
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<p align="center">option</p> |
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</td> |
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<td width="667"> |
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< |
<blockquote> |
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< |
<div align="center">description</div> |
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< |
</blockquote> |
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< |
</td> |
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< |
</tr> |
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< |
<tr bgcolor="#ccffcc"> |
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< |
<td> |
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<p align="center">--rcorr</p> |
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</td> |
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< |
<td>mean square displacement </td> |
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< |
</tr> |
| 508 |
< |
<tr bgcolor="#ccffcc"> |
| 509 |
< |
<td> |
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<p align="center">--vcorr</p> |
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</td> |
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<td>velocity autocorrelation function</td> |
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< |
</tr> |
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< |
<tr bgcolor="#ccffcc"> |
| 515 |
< |
<td> |
| 516 |
< |
<p align="center">--dcorr</p> |
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</td> |
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<td>dipole correlation function </td> |
| 519 |
< |
</tr> |
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< |
</tbody> |
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< |
</table> |
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< |
</ul> |
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<p> |
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</p> |
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</body> |
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</html> |
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> |
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<html> |
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<head> |
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<title>Selection syntax for OOPSE utility programs</title> |
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</head> |
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<body style="background-color: white;"> |
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<basefont size="3"> |
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<div align="center"> |
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<p><font size="+2"><b>Selection syntax for OOPSE utility programs</b></font><span |
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style="font-weight: bold;"></span><br> |
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</p> |
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<h2 align="left"><a name="introduction" id="introduction"> Introduction |
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> |
</a></h2> |
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<p style="text-align: left;">The OOPSE utility programs compute |
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> |
properties from the <span |
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> |
style="font-family: monospace; font-weight: bold;">dump</span><span |
| 17 |
> |
style="font-weight: bold;"> |
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> |
</span>files that are generated during a molecular dynamics |
| 19 |
> |
simulation. |
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> |
These programs are:<br> |
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</p> |
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<ul style="text-align: left;"> |
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<li><span style="font-family: monospace; font-weight: bold;">Dump2XYZ</span><span |
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> |
style="font-weight: bold;"> </span>- Converts an OOPSE dump file into |
| 25 |
> |
a file suitable |
| 26 |
> |
for viewing in a molecular dynamics viewer like <a |
| 27 |
> |
href="http://www.jmol.org">Jmol</a><br> |
| 28 |
> |
</li> |
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> |
<li><span style="font-family: monospace; font-weight: bold;">StaticProps</span><span |
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> |
style="font-weight: bold;"> </span>- Computes static properties like |
| 31 |
> |
the pair distribution function, <span style="font-style: italic;">g(r)</span>.<br> |
| 32 |
> |
</li> |
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> |
<li><span style="font-family: monospace; font-weight: bold;">DynamicProps</span><span |
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> |
style="font-weight: bold;"> </span>- Computes time correlation |
| 35 |
> |
functions like the |
| 36 |
> |
velocity autocorrelation function, <span style="font-style: italic;"><<span |
| 37 |
> |
style="font-weight: bold;">v</span>(t)<span style="font-weight: bold;">v</span>(0)></span>, |
| 38 |
> |
or the mean square displacement <span style="font-style: italic;"><|<span |
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> |
style="font-weight: bold;">r</span>(t) - <span |
| 40 |
> |
style="font-weight: bold;">r</span>(0)|<sup>2</sup>>.</span></li> |
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> |
</ul> |
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> |
<div style="text-align: left;">These programs often need to operate on |
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> |
a subset of the data contained within a dump file. For example, |
| 44 |
> |
if you want only the <span style="font-style: italic;">oxygen-oxygen</span> |
| 45 |
> |
pair distribution from a water simulation, or if you want to make a |
| 46 |
> |
movie including only the water molecules within a 6 angstrom radius of |
| 47 |
> |
lipid head groups, you need a way to specify your selection to these |
| 48 |
> |
utility programs. OOPSE has a selection syntax which allows |
| 49 |
> |
you to specify the selection in a compact form in order to generate |
| 50 |
> |
only the data you want. For example a common use of the |
| 51 |
> |
StaticProps command would be:<br> |
| 52 |
> |
<br> |
| 53 |
> |
<div style="margin-left: 80px;"><span |
| 54 |
> |
style="font-family: monospace; font-weight: bold;">StaticProps -i |
| 55 |
> |
tp4.dump --gofr --sele1="select O*" --sele2="select O*"</span><br> |
| 56 |
> |
</div> |
| 57 |
> |
<br> |
| 58 |
> |
This command computes the oxygen-oxygen pair distribution function, <span |
| 59 |
> |
style="font-style: italic;">g<sub>OO</sub>(r)</span>, from a file |
| 60 |
> |
named <span style="font-family: monospace;">tp4.dump</span>. In |
| 61 |
> |
order to understand this selection syntax and to make full use of the |
| 62 |
> |
selection capabilities of the analysis programs, it is necessary to |
| 63 |
> |
understand a few of the core concepts that are used to perform |
| 64 |
> |
simulations.<br> |
| 65 |
> |
<h2><a name="Concepts"></a>Concepts</h2> |
| 66 |
> |
OOPSE manipulates both traditional atoms as well as some objects that <span |
| 67 |
> |
style="font-style: italic;">behave like atoms</span>. These |
| 68 |
> |
objects can be rigid collections of atoms or atoms which have |
| 69 |
> |
orientational degrees of freedom. Here is a diagram of the class |
| 70 |
> |
heirarchy:<br> |
| 71 |
> |
<span style="font-style: italic;"></span></div> |
| 72 |
> |
<p align="center"><img src="classoopse_1_1StuntDouble.png" height="136" |
| 73 |
> |
width="292"><br> |
| 74 |
> |
</p> |
| 75 |
> |
<ul style="text-align: left;"> |
| 76 |
> |
<li>A <span style="font-family: monospace; font-weight: bold;">StuntDouble</span> |
| 77 |
> |
is <span style="font-style: italic;">any</span> object that can be |
| 78 |
> |
manipulated by the integrators and minimizers.</li> |
| 79 |
> |
<li>An <span style="font-family: monospace; font-weight: bold;">Atom</span> |
| 80 |
> |
is a fundamental point-particle that can be moved around during a |
| 81 |
> |
simulation.</li> |
| 82 |
> |
<li>A <span style="font-family: monospace; font-weight: bold;">DirectionalAtom</span> |
| 83 |
> |
is an atom which has <span style="font-style: italic;">orientational</span> |
| 84 |
> |
as well as translational degrees of freedom.</li> |
| 85 |
> |
<li>A <span style="font-family: monospace; font-weight: bold;">RigidBody</span> |
| 86 |
> |
is a collection of <span |
| 87 |
> |
style="font-family: monospace; font-weight: bold;">Atom</span>s or <span |
| 88 |
> |
style="font-family: monospace; font-weight: bold;">DirectionalAtom</span>s |
| 89 |
> |
which behaves as a <span style="font-style: italic;">single unit.</span></li> |
| 90 |
> |
</ul> |
| 91 |
> |
<p align="left"> Every Molecule, Atom and DirectionalAtom in OOPSE |
| 92 |
> |
have their own names which are specified in the <span |
| 93 |
> |
style="font-family: monospace; font-weight: bold;">.md</span> file. In |
| 94 |
> |
contrast, RigidBodies are denoted by their membership and index inside |
| 95 |
> |
a particular molecule: <span style="font-family: monospace;">[MoleculeName]_RB_[index]</span> |
| 96 |
> |
(the contents inside |
| 97 |
> |
the brackets depend on the specifics of the simulation). The names of |
| 98 |
> |
rigid bodies are generated automatically. For |
| 99 |
> |
example, the name of the first rigid body in a DMPC molecule is |
| 100 |
> |
DMPC_RB_0.<br> |
| 101 |
> |
</p> |
| 102 |
> |
</div> |
| 103 |
> |
<h2><a name="select"></a>Syntax of the Select Command</h2> |
| 104 |
> |
The most general form of the select command is: <b>select <i>expression</i> |
| 105 |
> |
</b> |
| 106 |
> |
<p>This expression represents an arbitrary set of StuntDoubles (Atoms |
| 107 |
> |
or |
| 108 |
> |
RigidBodies) in OOPSE. Expressions are composed of either name |
| 109 |
> |
expressions, index expression, predefined sets, user-defined |
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> |
expression, |
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> |
comparison operators, within expressions, or logical combinations of |
| 112 |
> |
the above expression types. Expression can be combined using |
| 113 |
> |
parentheses |
| 114 |
> |
and the Boolean operators</p> |
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> |
<p><b><a name="logic"></a> Logical expression. </b> </p> |
| 116 |
> |
<p>The logical operators allow complex queries to be constructed out of |
| 117 |
> |
simpler ones using the standard boolean connectives <b>and, or, not</b>. |
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> |
Parentheses can be used to alter the precedence of the operators. |
| 119 |
> |
</p> |
| 120 |
> |
<ul> |
| 121 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="441"> |
| 122 |
> |
<tbody> |
| 123 |
> |
<tr bgcolor="#ffccff"> |
| 124 |
> |
<td width="174"> |
| 125 |
> |
<div align="left">logical operator </div> |
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> |
</td> |
| 127 |
> |
<td width="241"> |
| 128 |
> |
<div align="left">equivalent operator</div> |
| 129 |
> |
</td> |
| 130 |
> |
</tr> |
| 131 |
> |
<tr bgcolor="#ffccff"> |
| 132 |
> |
<td> |
| 133 |
> |
<div align="left">and</div> |
| 134 |
> |
</td> |
| 135 |
> |
<td> |
| 136 |
> |
<div align="left">"&", "&&" </div> |
| 137 |
> |
</td> |
| 138 |
> |
</tr> |
| 139 |
> |
<tr bgcolor="#ffccff"> |
| 140 |
> |
<td> |
| 141 |
> |
<div align="left">or</div> |
| 142 |
> |
</td> |
| 143 |
> |
<td> |
| 144 |
> |
<div align="left">"|", "||", "," </div> |
| 145 |
> |
</td> |
| 146 |
> |
</tr> |
| 147 |
> |
<tr bgcolor="#ffccff"> |
| 148 |
> |
<td> |
| 149 |
> |
<div align="left">not</div> |
| 150 |
> |
</td> |
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> |
<td> |
| 152 |
> |
<div align="left">"!"</div> |
| 153 |
> |
</td> |
| 154 |
> |
</tr> |
| 155 |
> |
</tbody> |
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> |
</table> |
| 157 |
> |
<p> </p> |
| 158 |
> |
</ul> |
| 159 |
> |
<p><a name="name"><b> Name expression. |
| 160 |
> |
</b></a> </p> |
| 161 |
> |
<ul> |
| 162 |
> |
<table bgcolor="#ffffcc" border="1" bordercolor="#6b7683" width="886"> |
| 163 |
> |
<tbody> |
| 164 |
> |
<tr> |
| 165 |
> |
<td colspan="2"> |
| 166 |
> |
<div align="center">expression</div> |
| 167 |
> |
</td> |
| 168 |
> |
<td width="434"> |
| 169 |
> |
<div align="center">description</div> |
| 170 |
> |
</td> |
| 171 |
> |
</tr> |
| 172 |
> |
<tr> |
| 173 |
> |
<td rowspan="3" width="183">expression without "." </td> |
| 174 |
> |
<td width="247"> |
| 175 |
> |
<div align="left">select DMPC</div> |
| 176 |
> |
</td> |
| 177 |
> |
<td>select all StuntDoubles belonging to all DMPC molecules </td> |
| 178 |
> |
</tr> |
| 179 |
> |
<tr> |
| 180 |
> |
<td> |
| 181 |
> |
<div align="left">select C*</div> |
| 182 |
> |
</td> |
| 183 |
> |
<td>select all atoms which have atom types beginning with C<br> |
| 184 |
> |
</td> |
| 185 |
> |
</tr> |
| 186 |
> |
<tr> |
| 187 |
> |
<td> |
| 188 |
> |
<div align="left">select DMPC_RB_*</div> |
| 189 |
> |
</td> |
| 190 |
> |
<td>select all RigidBodies in DMPC molecules (only select |
| 191 |
> |
rigid-bodies, but not |
| 192 |
> |
include the atoms belong to them)</td> |
| 193 |
> |
</tr> |
| 194 |
> |
<tr> |
| 195 |
> |
<td rowspan="3">expression has one "." </td> |
| 196 |
> |
<td>select TIP3P.O_TIP3P</td> |
| 197 |
> |
<td>select the O_TIP3P Atoms belong to TIP3P molecules </td> |
| 198 |
> |
</tr> |
| 199 |
> |
<tr> |
| 200 |
> |
<td>select DMPC_RB_0.PO4</td> |
| 201 |
> |
<td>select the PO4 Atoms belonging to first RigidBody in each |
| 202 |
> |
DMPC molecule<br> |
| 203 |
> |
</td> |
| 204 |
> |
</tr> |
| 205 |
> |
<tr> |
| 206 |
> |
<td>select DMPC.20</td> |
| 207 |
> |
<td>select the 20th StuntDouble in each DMPC molecule<br> |
| 208 |
> |
</td> |
| 209 |
> |
</tr> |
| 210 |
> |
<tr> |
| 211 |
> |
<td>expression has two "."</td> |
| 212 |
> |
<td>select DMPC.DMPC_RB_?.*</td> |
| 213 |
> |
<td>select all Atoms belonging to all rigid-bodies within all |
| 214 |
> |
DMPC molecules</td> |
| 215 |
> |
</tr> |
| 216 |
> |
</tbody> |
| 217 |
> |
</table> |
| 218 |
> |
<p> </p> |
| 219 |
> |
</ul> |
| 220 |
> |
<p><a name="index" id="index"><b> Index expression </b></a></p> |
| 221 |
> |
<ul> |
| 222 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="894"> |
| 223 |
> |
<tbody> |
| 224 |
> |
<tr bgcolor="#ffffcc"> |
| 225 |
> |
<td width="113">select 20 </td> |
| 226 |
> |
<td width="520">select all of the StuntDoubles belonging to |
| 227 |
> |
Molecule 20</td> |
| 228 |
> |
</tr> |
| 229 |
> |
<tr bgcolor="#ffffcc"> |
| 230 |
> |
<td>select 20 to 30 </td> |
| 231 |
> |
<td>select all of the StuntDoules belonging to molecules which |
| 232 |
> |
have global |
| 233 |
> |
indices between 20 (inclusive) and 30 (exclusive) </td> |
| 234 |
> |
</tr> |
| 235 |
> |
</tbody> |
| 236 |
> |
</table> |
| 237 |
> |
</ul> |
| 238 |
> |
<p> </p> |
| 239 |
> |
<p><a name="predefine" id="predefine"><b> Predefined sets </b></a></p> |
| 240 |
> |
<ul> |
| 241 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="449"> |
| 242 |
> |
<tbody> |
| 243 |
> |
<tr bgcolor="#ffccff"> |
| 244 |
> |
<td width="91"> |
| 245 |
> |
<div align="left">keyword</div> |
| 246 |
> |
</td> |
| 247 |
> |
<td width="332"> |
| 248 |
> |
<div align="left">description</div> |
| 249 |
> |
</td> |
| 250 |
> |
</tr> |
| 251 |
> |
<tr bgcolor="#ffccff"> |
| 252 |
> |
<td> |
| 253 |
> |
<div align="left">all</div> |
| 254 |
> |
</td> |
| 255 |
> |
<td> |
| 256 |
> |
<div align="left">select all StuntDoubles</div> |
| 257 |
> |
</td> |
| 258 |
> |
</tr> |
| 259 |
> |
<tr bgcolor="#ffccff"> |
| 260 |
> |
<td> |
| 261 |
> |
<div align="left">none</div> |
| 262 |
> |
</td> |
| 263 |
> |
<td> |
| 264 |
> |
<div align="left">select none of the StuntDoubles </div> |
| 265 |
> |
</td> |
| 266 |
> |
</tr> |
| 267 |
> |
</tbody> |
| 268 |
> |
</table> |
| 269 |
> |
</ul> |
| 270 |
> |
<p> </p> |
| 271 |
> |
<p><a name="user" id="user"><b> User defined expressions</b></a></p> |
| 272 |
> |
<p> Users can define arbitrary terms to represent groups of |
| 273 |
> |
StuntDoubles, and then use the define terms in select |
| 274 |
> |
commands. The general form for the define command is: <strong>define <em>term |
| 275 |
> |
expression</em></strong></p> |
| 276 |
> |
<p> Once defined, the user can specify such terms in boolean |
| 277 |
> |
expressions </p> |
| 278 |
> |
<ul> |
| 279 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="659"> |
| 280 |
> |
<tbody> |
| 281 |
> |
<tr bgcolor="#ffffcc"> |
| 282 |
> |
<td> |
| 283 |
> |
<p>define SSDWATER SSD or SSD1 or SSDRF</p> |
| 284 |
> |
<p>select SSDWATER </p> |
| 285 |
> |
</td> |
| 286 |
> |
</tr> |
| 287 |
> |
</tbody> |
| 288 |
> |
</table> |
| 289 |
> |
</ul> |
| 290 |
> |
<p><a name="comparison" id="comparison"> <b>Comparison expression.</b></a></p> |
| 291 |
> |
<p>StuntDoubles can be selected by using comparision operators on |
| 292 |
> |
their properties. The general form for the comparison command is: a |
| 293 |
> |
property name, followed by a comparision operator and then a number.</p> |
| 294 |
> |
<ul> |
| 295 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="668"> |
| 296 |
> |
<tbody> |
| 297 |
> |
<tr bgcolor="#ffccff"> |
| 298 |
> |
<td width="305"> |
| 299 |
> |
<div align="left">property</div> |
| 300 |
> |
</td> |
| 301 |
> |
<td width="331"> |
| 302 |
> |
<div align="left">mass, charge </div> |
| 303 |
> |
</td> |
| 304 |
> |
</tr> |
| 305 |
> |
<tr bgcolor="#ffccff"> |
| 306 |
> |
<td> |
| 307 |
> |
<div align="left">comparision operator</div> |
| 308 |
> |
</td> |
| 309 |
> |
<td> |
| 310 |
> |
<div align="left">">", "<", "=", ">=", "<=", "!=" </div> |
| 311 |
> |
</td> |
| 312 |
> |
</tr> |
| 313 |
> |
</tbody> |
| 314 |
> |
</table> |
| 315 |
> |
</ul> |
| 316 |
> |
<ul> |
| 317 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="672"> |
| 318 |
> |
<tbody> |
| 319 |
> |
<tr bgcolor="#ffffcc"> |
| 320 |
> |
<td width="302">select mass > 16.0 and charge < -2 </td> |
| 321 |
> |
<td width="338">select StuntDoubles which have mass greater |
| 322 |
> |
than |
| 323 |
> |
16.0 and charges less than -2 </td> |
| 324 |
> |
</tr> |
| 325 |
> |
</tbody> |
| 326 |
> |
</table> |
| 327 |
> |
</ul> |
| 328 |
> |
<p> </p> |
| 329 |
> |
<p><b> <a name="within"></a> Within expression.</b> |
| 330 |
> |
</p> |
| 331 |
> |
<p> The "within" selection allows the user to select all StuntDoubles |
| 332 |
> |
within the specified |
| 333 |
> |
distance (in Angstroms) from a selection, including the selected atom |
| 334 |
> |
itself. The |
| 335 |
> |
general form for within selection is: <b>select within(<i>distance, |
| 336 |
> |
expression</i>) </b> |
| 337 |
> |
</p> |
| 338 |
> |
<ul> |
| 339 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="681"> |
| 340 |
> |
<tbody> |
| 341 |
> |
<tr bgcolor="#ffffcc"> |
| 342 |
> |
<td width="306">select within(2.5, PO4 or NC4) </td> |
| 343 |
> |
<td width="343"> |
| 344 |
> |
<blockquote>select all StuntDoubles which are within 2.5 |
| 345 |
> |
angstroms of PO4 or NC4 atoms<br> |
| 346 |
> |
</blockquote> |
| 347 |
> |
</td> |
| 348 |
> |
</tr> |
| 349 |
> |
</tbody> |
| 350 |
> |
</table> |
| 351 |
> |
</ul> |
| 352 |
> |
<p> |
| 353 |
> |
</p> |
| 354 |
> |
<h2><a name="syntax" id="syntax"> Tools which use the selection command |
| 355 |
> |
</a></h2> |
| 356 |
> |
<p><b><a name="within"></a> Dump2XYZ</b> |
| 357 |
> |
</p> |
| 358 |
> |
<p>Dump2XYZ can transform an OOPSE dump file into a xyz file which |
| 359 |
> |
could be opened by other molecular viewers, such as Jmol and VMD. </p> |
| 360 |
> |
<ul> |
| 361 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="890"> |
| 362 |
> |
<tbody> |
| 363 |
> |
<tr bgcolor="#6699ff"> |
| 364 |
> |
<td width="191"> |
| 365 |
> |
<blockquote> |
| 366 |
> |
<p>--selection</p> |
| 367 |
> |
</blockquote> |
| 368 |
> |
</td> |
| 369 |
> |
<td width="667">Specifying --selection="selection command" with |
| 370 |
> |
Dump2XYZ, user can select an arbitrary set of stuntdoubles to be |
| 371 |
> |
converted. </td> |
| 372 |
> |
</tr> |
| 373 |
> |
<tr bgcolor="#ccff99"> |
| 374 |
> |
<td> |
| 375 |
> |
<blockquote> |
| 376 |
> |
<p>--originsele</p> |
| 377 |
> |
</blockquote> |
| 378 |
> |
</td> |
| 379 |
> |
<td rowspan="2">In order to rotate the system, --originsele and |
| 380 |
> |
--refselec must be given to define the new coordinate set. A |
| 381 |
> |
stuntdouble with a dipole, which direction is always (0, 0, 1) in body |
| 382 |
> |
frame, is specified by --originsele. The new x-z plane is defined by |
| 383 |
> |
the direction of dipole and the StuntDouble is specified by --refsele. </td> |
| 384 |
> |
</tr> |
| 385 |
> |
<tr bgcolor="#ccff99"> |
| 386 |
> |
<td> |
| 387 |
> |
<blockquote> |
| 388 |
> |
<p>--refsele</p> |
| 389 |
> |
</blockquote> |
| 390 |
> |
</td> |
| 391 |
> |
</tr> |
| 392 |
> |
</tbody> |
| 393 |
> |
</table> |
| 394 |
> |
</ul> |
| 395 |
> |
<p> |
| 396 |
> |
</p> |
| 397 |
> |
<p><b><a name="within"></a> StaticProps<br> |
| 398 |
> |
</b></p> |
| 399 |
> |
StaticProps can compute properties which are averaged over the |
| 400 |
> |
configurations that are contained within a dump file. The |
| 401 |
> |
most common example of a static property that can be computed is the |
| 402 |
> |
pair distribution function between atoms of type A and other atoms of |
| 403 |
> |
type B, <span style="font-style: italic;">g<sub>AB</sub>(r)</span>. |
| 404 |
> |
StaticProps can also be used to compute the density distributions of |
| 405 |
> |
other molecules in a reference frame <span style="font-style: italic;">fixed |
| 406 |
> |
to the body-fixed reference frame</span> of a selected atom or rigid |
| 407 |
> |
body.<b><br> |
| 408 |
> |
</b> |
| 409 |
> |
<p> </p> |
| 410 |
> |
<p align="center"><img src="definition.jpg" height="540" width="720"></p> |
| 411 |
> |
<p align="left">There are five seperate radial distribution functions |
| 412 |
> |
availiable in OOPSE. Since every radial distrbution function invlove |
| 413 |
> |
the calculation between a pair, --sele1 and --sele2 must be given. |
| 414 |
> |
</p> |
| 415 |
> |
<ul> |
| 416 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="890"> |
| 417 |
> |
<tbody> |
| 418 |
> |
<tr bgcolor="#ccffcc"> |
| 419 |
> |
<td width="191"> |
| 420 |
> |
<blockquote> |
| 421 |
> |
<p>option</p> |
| 422 |
> |
</blockquote> |
| 423 |
> |
</td> |
| 424 |
> |
<td width="667"> |
| 425 |
> |
<blockquote> |
| 426 |
> |
<div align="center">description</div> |
| 427 |
> |
</blockquote> |
| 428 |
> |
</td> |
| 429 |
> |
</tr> |
| 430 |
> |
<tr bgcolor="#ccffcc"> |
| 431 |
> |
<td> |
| 432 |
> |
<blockquote> |
| 433 |
> |
<p>--gofr</p> |
| 434 |
> |
</blockquote> |
| 435 |
> |
</td> |
| 436 |
> |
<td>Computes the pair distribution function.</td> |
| 437 |
> |
</tr> |
| 438 |
> |
<tr bgcolor="#ccffcc"> |
| 439 |
> |
<td> |
| 440 |
> |
<blockquote> |
| 441 |
> |
<p>--r_theta</p> |
| 442 |
> |
</blockquote> |
| 443 |
> |
</td> |
| 444 |
> |
<td>Computes the angle-dependent pair distribution function. |
| 445 |
> |
The |
| 446 |
> |
angle is defined by the intermolecular vector r and z-axis of |
| 447 |
> |
DirectionalAtom A.<br> |
| 448 |
> |
</td> |
| 449 |
> |
</tr> |
| 450 |
> |
<tr bgcolor="#ccffcc"> |
| 451 |
> |
<td> |
| 452 |
> |
<blockquote> |
| 453 |
> |
<p>--r_omega</p> |
| 454 |
> |
</blockquote> |
| 455 |
> |
</td> |
| 456 |
> |
<td>Computes an angle-dependent pair distribution function. The |
| 457 |
> |
angle is defined by the z-axes of the two DirectionalAtoms A and B.<br> |
| 458 |
> |
</td> |
| 459 |
> |
</tr> |
| 460 |
> |
<tr bgcolor="#ccffcc"> |
| 461 |
> |
<td> |
| 462 |
> |
<blockquote> |
| 463 |
> |
<p>--theta_omega</p> |
| 464 |
> |
</blockquote> |
| 465 |
> |
</td> |
| 466 |
> |
<td>Calculate the pair distribution of the two angles.</td> |
| 467 |
> |
</tr> |
| 468 |
> |
<tr bgcolor="#ccffcc"> |
| 469 |
> |
<td> |
| 470 |
> |
<blockquote> |
| 471 |
> |
<p>--gxyz</p> |
| 472 |
> |
</blockquote> |
| 473 |
> |
</td> |
| 474 |
> |
<td>Calculate the density distribution of particles |
| 475 |
> |
of type B in the body frame of particle A. Therefore, --originsele and |
| 476 |
> |
--refsele must be given to define A's internal coordinate set. </td> |
| 477 |
> |
</tr> |
| 478 |
> |
</tbody> |
| 479 |
> |
</table> |
| 480 |
> |
</ul> |
| 481 |
> |
<p> </p> |
| 482 |
> |
<p><b><a name="within"></a> DynamicProps<br> |
| 483 |
> |
<span style="font-weight: bold;"><br> |
| 484 |
> |
</span></b>DynamicProps computes time correlation functions from the |
| 485 |
> |
configurations stored in a dump file. Typical examples of time |
| 486 |
> |
correlation functions are the mean square displacement and the velocity |
| 487 |
> |
autocorrelation functions. <b><span style="font-weight: bold;"><br> |
| 488 |
> |
</span> </b></p> |
| 489 |
> |
<ul> |
| 490 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="890"> |
| 491 |
> |
<tbody> |
| 492 |
> |
<tr bgcolor="#ccffcc"> |
| 493 |
> |
<td width="191"> |
| 494 |
> |
<p align="center">option</p> |
| 495 |
> |
</td> |
| 496 |
> |
<td width="667"> |
| 497 |
> |
<blockquote> |
| 498 |
> |
<div align="center">description</div> |
| 499 |
> |
</blockquote> |
| 500 |
> |
</td> |
| 501 |
> |
</tr> |
| 502 |
> |
<tr bgcolor="#ccffcc"> |
| 503 |
> |
<td> |
| 504 |
> |
<p align="center">--rcorr</p> |
| 505 |
> |
</td> |
| 506 |
> |
<td>mean square displacement </td> |
| 507 |
> |
</tr> |
| 508 |
> |
<tr bgcolor="#ccffcc"> |
| 509 |
> |
<td> |
| 510 |
> |
<p align="center">--vcorr</p> |
| 511 |
> |
</td> |
| 512 |
> |
<td>velocity autocorrelation function</td> |
| 513 |
> |
</tr> |
| 514 |
> |
<tr bgcolor="#ccffcc"> |
| 515 |
> |
<td> |
| 516 |
> |
<p align="center">--dcorr</p> |
| 517 |
> |
</td> |
| 518 |
> |
<td>dipole correlation function </td> |
| 519 |
> |
</tr> |
| 520 |
> |
</tbody> |
| 521 |
> |
</table> |
| 522 |
> |
</ul> |
| 523 |
> |
<p> |
| 524 |
> |
</p> |
| 525 |
> |
</body> |
| 526 |
> |
</html> |
