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<title>Select Commands in OOPSE</title> |
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</head> |
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<body bgcolor=white> |
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<basefont size=3> |
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<div align=center> |
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<p><font size="+2"><b>Select Commands in </b></font><b><font size="+2">OOPSE</font></b></p> |
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<h2 align="left"><a name="introduction" id="introduction"> Introduction </a></h2> |
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<p align="left"> </p> |
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<p align="center"><img src="classoopse_1_1StuntDouble.png" width="292" height="136"></p> |
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<p align="left"><b><a name="stuntdouble" id="stuntdouble"></a> Stuntdouble </b> stands in for some object that can be manipulated by the Integrators or Minimizers. </p> |
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<p align="left"><b><a name="atom" id="atom"></a> Atom </b>is a fundamental unit in OOPSE</p> |
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<p align="left"><b><a name="datom" id="datom"></a> DirectionalAtom </b>is a special atom</p> |
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<p align="left"><b><a name="rigidbody" id="rigidbody"></a> Rigid-body </b>is a collection of atoms or directional atoms. </p> |
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<p align="left"> Every molecule, atom and directional atom in OOPSE have their own name which are given by .md file. In contrast, the name of rigid-body, which is [MoleculeName]_RB_[index] (the content inside the brackets will be replaced), is generated automatically. For example, the name of the first rigi-body of DMPC molecule is DMPC_RB_0. <br> |
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</p> |
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</div> |
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<a name="syntax" id="syntax"> |
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<h2> |
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Syntax of the select command |
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</h2> |
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</a> |
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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>The expression represents an arbitrary set of stuntdoubles (atoms or rigid-bodies) in OOPSE. Expressions are composed of either name expressions, index expression, predefined sets, user define expression, comparison operators, within expressions, or logical combinations of the above expression types. Expression can be combined with parentheses 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 simpler ones using the standard boolean connectives <b>and, or, not</b>. Parentheses can be used to alter the precedence of the operators. |
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<ul> |
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<table width="441" border=1 cellpadding=5 bgcolor="#FFFFFF"> |
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<td width="174"><div align="left">logical operator </div></td> |
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<td width="241"><div align="left">equivalent operator</div></td> |
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</tr> |
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<tr bgcolor="#FFCCFF"> |
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<td><div align="left">and</div></td> |
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<td><div align="left">"&", "&&" </div></td> |
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</tr> |
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<tr bgcolor="#FFCCFF"> |
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<td><div align="left">or</div></td> |
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<td><div align="left">"|", "||", "," </div></td> |
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</tr> |
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<tr bgcolor="#FFCCFF"> |
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<td><div align="left">not</div></td> |
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<td><div align="left">"!"</div></td> |
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</tr> |
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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 width="886" border="1" bordercolor="#6B7683" bgcolor="#FFFFCC"> |
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<td colspan="2"><div align="center">expression</div></td> |
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<td width="434"><div align="center">description</div></td> |
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</tr> |
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<td width="183" rowspan="3">expression without "." </td> |
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<td width="247"><div align="left">select DMPC</div></td> |
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<td>select all stuntdoubles belong to DMPC molecule </td> |
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</tr> |
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<tr> |
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<td><div align="left">select C*</div></td> |
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<td>select all carbon atoms </td> |
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</tr> |
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<td><div align="left">select DMPC_RB_*</div></td> |
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<td>select all rigid-bodies (only select rigid-bodies, not include the atoms belong to them)</td> |
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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 stuntdoubles belong to molecule </td> |
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</tr> |
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<td>select DMPC_RB_0.PO4</td> |
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<td>select atoms belong to rigid-bodies</td> |
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</tr> |
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<td>select DMPC.20</td> |
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<td>select stuntdoubles by their internal indices inside the molecules </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 belong to rigid-bodies within DMPC molecule</td> |
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</tr> |
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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 width="894" border=1 cellpadding=5 bgcolor="#FFFFFF"><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 of 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 stuntdoubles of molecules which global indices are between 20 (inclusive) and 30 (exclusive) </td> |
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</tr> |
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</table> |
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<p> </p> |
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<p><a name="predefine" id="predefine"><b> Predefine set </b></a></p> |
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<ul> |
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<table width="449" border=1 cellpadding=5 bgcolor="#FFFFFF"> |
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<tr bgcolor="#FFCCFF"> |
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<td width="91"><div align="left">keyword</div></td> |
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<td width="332"><div align="left">description</div></td> |
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</tr> |
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<td><div align="left">all</div></td> |
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<td><div align="left">select all stuntdoubles</div></td> |
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</tr> |
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<tr bgcolor="#FFCCFF"> |
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<td><div align="left">none</div></td> |
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<td><div align="left">select none of the stuntdoubles </div></td> |
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</tr> |
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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 define expression.</b></a></p> |
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<p> User can define arbitrary terms to represent groups of stuntdoubles, and then use the terms you have defined in select commands. The general form for the define command is: <strong>define <em>term expression</em></strong></p> |
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<p> Once defined, user can use such terms in boolean expressions </p> |
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<table width="659" border=1 cellpadding=5 bgcolor="#FFFFFF"> |
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<td><p>define SSDWATER SSD or SSD1 or SSDRF</p> |
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<p>select SSDWATER </p> <div align="left"></div></td> |
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</tr> |
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</table> |
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<p><a name="comparison" id="comparison"> <b>Comparison expression.</b></a></p> |
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<p>Stuntdoubles can be distinguished using comparision operators on their properties. The general form for the comparison command is: a property name, followed by a comparision operator and then a number.</p> |
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<ul> |
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<table width="668" border=1 cellpadding=5 bgcolor="#FFFFFF"> |
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<td width="305"><div align="left">property</div></td> |
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<td width="331"><div align="left">mass, dipole, charge </div></td> |
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</tr> |
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<tr bgcolor="#FFCCFF"> |
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<td><div align="left">comparision operator</div></td> |
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<td><div align="left">">", "<", "=", ">=", "<=", "!=" </div></td> |
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</tr> |
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</table> |
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<table width="672" border=1 cellpadding=5 bgcolor="#FFFFFF"> |
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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 mass is great than 16.0 and charge is less than -2 </td> |
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</table> |
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<p> </p> |
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<p><b> <a name="within"></a> Within expression.</b> |
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<p> Within selection selects all stuntdoubles within the specified distance (in ?) from a selection, including the selection itself. The general form for within selection is: <b>select within(<i>distance, expression</i>) </b> |
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<ul> |
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<table width="681" border=1 cellpadding=5 bgcolor="#FFFFFF"> |
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<td width="306">select within(2.5, PO4 or NC4) </td> |
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<td width="343"><blockquote>select stunntdoules which are within 2.5 ? from either PO4 or NC4 </blockquote></td> |
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</tr> |
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</table> |
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</ul> |
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<p> |
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<h2><a name="syntax" id="syntax"> Tools using selection command </a></h2> |
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<p><b><a name="within"></a> Dump2XYZ</b> |
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<p>Dump2XYZ can transform an OOPSE dump file into a xyz file which could be opened by other molecular viewers, such as Jmol and VMD. |
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<ul> |
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<table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF"> |
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<tr bgcolor="#6699FF"> |
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<td width="191"><blockquote> |
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<p>--selection</p> |
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</blockquote></td> |
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<td width="667">Specifying --selection="selection command" with Dump2XYZ, user can select an arbitrary set of stuntdoubles to be converted. </td> |
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</tr> |
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<tr bgcolor="#CCFF99"> |
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<td><blockquote> |
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<p>--originsele</p> |
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</blockquote></td> |
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<td rowspan="2">In order to rotate the system, --originsele and --refselec must be given to define the new coordinate set. A stuntdouble with a dipole, which direction is always (0, 0, 1) in body frame, is specified by --originsele. The new x-z plane is defined by the direction of dipole and the stuntdouble specified by --refsele. </td> |
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</tr> |
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<tr bgcolor="#CCFF99"> |
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<td><blockquote> |
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<p>--refsele</p> |
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</blockquote></td> |
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</tr> |
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</table> |
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</ul> |
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<p> |
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<p><b><a name="within"></a> StaticProps</b> |
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<p> |
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<p align="center"><img src="definition.jpg" width="720" height="540"> |
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<p align="left">There are five seperate radial distribution functions availiable in OOPSE. Since every radial distrbution function invlove the calculation between a pair, --sele1 and --sele2 must be given. |
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<ul> |
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<table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF"> |
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<tr bgcolor="#CCFFCC"> |
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<td width="191"><blockquote> |
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<p>option</p> |
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</blockquote></td> |
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<td width="667"><blockquote> |
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<div align="center">description</div> |
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</blockquote></td> |
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</tr> |
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<tr bgcolor="#CCFFCC"> |
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<td><blockquote> |
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<p>--gofr</p> |
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</blockquote></td> |
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<td>normal pair distribution function.</td> |
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</tr> |
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<tr bgcolor="#CCFFCC"> |
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<td><blockquote> |
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<p>--r_theta</p> |
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</blockquote></td> |
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<td>Calculate angle dependent pair distribution function. The angle is defined by r and A's dipole moment. </td> |
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</tr> |
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<tr bgcolor="#CCFFCC"> |
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<td><blockquote> |
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<p>--r_omega</p> |
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</blockquote></td> |
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<td>Calculate angle dependent pair distribution function. The angle is defined by A's dipole moment and B's dipole moment . </td> |
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</tr> |
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<tr bgcolor="#CCFFCC"> |
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<td><blockquote> |
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<p>--theta_omega</p> |
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</blockquote></td> |
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<td>Calculate the two dimension distribution of two angles.</td> |
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</tr> |
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<tr bgcolor="#CCFFCC"> |
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<td><blockquote> |
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<p>--gxyz</p> |
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</blockquote></td> |
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<td>Calculate the three dimension distribution of the particle B in the body frame of particle A. Therefore, --originsele and --refsele must be given to define A's internal coordinate set. </td> |
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</tr> |
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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 </b> |
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<ul> |
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<table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF"> |
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<tr bgcolor="#CCFFCC"> |
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<td width="191"> <p align="center">option</p></td> |
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<td width="667"><blockquote> |
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<div align="center">description</div> |
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</blockquote></td> |
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</tr> |
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<tr bgcolor="#CCFFCC"> |
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<td> <p align="center">--rcorr</p></td> |
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<td>mean square displacement </td> |
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</tr> |
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<tr bgcolor="#CCFFCC"> |
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<td> <p align="center">--vcorr</p></td> |
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<td>velocity correlation function</td> |
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</tr> |
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<tr bgcolor="#CCFFCC"> |
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<td> <p align="center">--dcorr</p></td> |
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<td>dipole correlation function </td> |
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</tr> |
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</table> |
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</ul> |
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<p> |
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</body> |
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|
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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 |
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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> |
| 294 |
> |
<ul> |
| 295 |
> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="668"> |
| 296 |
> |
<tbody> |
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> |
<tr bgcolor="#ffccff"> |
| 298 |
> |
<td width="305"> |
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> |
<div align="left">property</div> |
| 300 |
> |
</td> |
| 301 |
> |
<td width="331"> |
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> |
<div align="left">mass, dipole, 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> |
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> |
<p> </p> |
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> |
<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> |
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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 |
| 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> |
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> |
<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> |
