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Hi Dan,<br>
<br>
Thanks for information it is working nicely.<br>
<br>
Now i wanted to try to put 2 ico rigid bodies next to each other.
But i am getting following error while simulation + Error when i am
converting it to XYZ via Dump2XYZ<br>
<br>
Can you give me hint? Files are attached<br>
<br>
<br>
OpenMD info:<br>
ForceManager::setupCutoffs: No value was set for the
cutoffPolicy.<br>
OpenMD will use TRADITIONAL.<br>
<br>
OpenMD info:<br>
StatWriter detected a numerical error writing: Total Energy
<br>
Converting Dump to XYZ ...<br>
OpenMD FATAL ERROR:<br>
DumpReader: Ico.dump does not contain a valid frame<br>
<br>
<br>
Ciao<br>
<br>
Martin<br>
<br>
<div class="moz-cite-prefix">On 27.11.2014 20:46, Dan Gezelter
wrote:<br>
</div>
<blockquote cite="mid:6AD5CC50-4280-428A-99D3-C2D13086A944@nd.edu"
type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">1. How can i add other atoms to interact with this Ico rigid body. And what do i need to add to Martin.frc file to setup interaction. Is it enough to setup forces? Like it is explained in openmd manual.
</pre>
</blockquote>
<pre wrap="">
Yes, you just need to make entries for the new atom types in the frc file and to provide some interaction model between the atoms on the RB and the other atoms. You'll also need a molecule definition, a component, and entries in the <Snapshot>. See the new demo files attached below.
</pre>
<blockquote type="cite">
<pre wrap="">2. How can i make my rigid body fixed in positions (no movements) and when it will interact with other (new atoms), it will not move.
</pre>
</blockquote>
<pre wrap="">
You could make a few (or all) of the atoms in the rigid body super heavy (i.e. change their mass to 10000 or more). We sometimes do this for nanoparticle simulations to prevent brownian motion of the particles away from a fixed location. You'll need more than one heavy atom if you want it to stop rotating as well. You could also add positional and orientational restraints, but these are harmonic restoring forces, so they will allow some motion.
Best regards,
--Dan
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<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">
Thanks again
Ciao
Martin
On 27.11.2014 20:05, Dan Gezelter wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Martin,
You do need to define the atom type in a force field file, and the force field can be quite a bit simpler than Amber for testing. The other issue I saw was that the quaternions in this line:
0 pvqj 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -1.8e-05 1.6e-06 1.9e-05
only had 3 entries. There should be 3 positions, 3 velocities, 4 quaternions, and 3 angular momentum variables. The convention we use for quaternions is defined on page 88 of Allen & Tildesley's "Computer Simulation of Liquids" book. To orient the principal body axis along the z-spatial coordinate, we could choose the following Euler angles:
\theta = 0
\phi = 0
\psi = 0
These correspond to a set of quaternions q = (1, 0, 0, 0).
Anyway, I tested the three attached files, and you should be able to experiment further with these. A couple of changes I made: 1) The _ (underscore) character has special meaning in the selection syntax, so I modified your atom types and rigid body definition. 2) The angular momentum was quite small, so I boosted it a bit so that you can observe the rotation in this simulation.
Try this with the attached files:
openmd Ico.md
Dump2XYZ -i Ico.dump
jmol Ico.xyz then go to "Tools" -> "Animate" -> "Once"
Best regards,
--Dan Gezelter
</pre>
<blockquote type="cite">
<pre wrap="">On Nov 26, 2014, at 11:01 PM, Martin Vala <a class="moz-txt-link-rfc2396E" href="mailto:mvala@saske.sk"><mvala@saske.sk></a>
wrote:
Hi all,
i just notice that i didn't define rigid body in my previous configuration. I am attaching my updated config files. I am sorry for wrong configuration files.
Ciao
Martin
On 27.11.2014 11:37, Martin Vala wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi All,
sorry i misstyped my rigid body. It is icosahedron
Ciao
Martin
On 27.11.2014 11:12, Martin Vala wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear OpenMD users,
I would like to define my own rigid body with my own atoms (my custom atom is "My"). My rigid body is defined as icohexadral (in RB_My.md file - attached). I am also attaching RigidBody_01.md file.
Problem:
OpenMD FATAL ERROR:
Can not find Matching Atom Type for[My_RB]
I am guessing that "My_RB" atom type is not defined in $FORCE_PARAM_PATH/Amber.frc (in my RB_My.md, i have forceField = "Amber";). So i will have to define my own MyForceField.frc file (or i will update Amber.frc file),where i will define "My" atom and whole force field defined in my this rigid body (probably define atom atom "My" and its interactions with others, e.g. interaction between atom "My" and "My", "My" and others, and so). Is it right?
If yes, then as first task, i would need to configure this rigid body to be fixed in its initial positions. Can you help me to set it up?
Thank you very much
Ciao
Martin
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<pre wrap="">
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</blockquote>
<pre wrap=""><RB_My.md><RigidBody_01.md>_______________________________________________
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