<p>Thanks, Justin. How to use "index groups"? Do I do it in .mdp file or use some program in tools/?</p><p>Luke<br></p><p><br></p><b>Justin A. Lemkul</b>
<a href="mailto:gmx-users%40gromacs.org?Subject=%5Bgmx-users%5D%20restraints%20between%20two%20molecules&In-Reply-To=CAJLK-9VYnde6D7SxY_eOLbQbTkoQmrTSn%3Dme2a%2Bdj4Q1h%3DsKEg%40mail.gmail.com" title="[gmx-users] restraints between two molecules">jalemkul at vt.edu
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<i>Fri Dec 2 18:04:37 CET 2011</i>
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<pre>lq z wrote:
><i> Dear GMXers,
</i>><i>
</i>><i> I can apply harmonic bond, angle, and dihedral restraints between two
</i>><i> molecules (3 atoms on one, and one atom on the other one). If yes, how
</i>><i> to set it up in the topology file?
</i>><i>
</i>
They have to be in the same [moleculetype].
><i> Question 2: Can I apply distance restraint between mass center of some
</i>><i> atoms in one molecule and ONE ATOM in the other molecule?
</i>><i>
</i>
Yes, with the pull code and suitable index groups.
><i> Question 3: Can those restraints be lambda (in alchemical free energy
</i>><i> simulation) dependent?
</i>><i>
</i>
Yes, see the manual.
-Justin
><i> You may have known what I'm trying to do: Change one molecule to dummy,
</i>><i> so I need restrain it at dummy state while no restraint is wanted at
</i>><i> real state.
</i>><i>
</i>><i> Thanks,
</i>><i> Luke
</i>><i>
</i>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>
========================================
</pre><br><br><div class="gmail_quote">On Fri, Dec 2, 2011 at 11:59 AM, lq z <span dir="ltr"><<a href="mailto:lqz.fsu@gmail.com">lqz.fsu@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Dear GMXers,<br><br>I can apply harmonic bond, angle, and dihedral restraints between two molecules (3 atoms on one, and one atom on the other one). If yes, how to set it up in the topology file? <br><br>Question 2: Can I apply distance restraint between mass center of some atoms in one molecule and ONE ATOM in the other molecule?<br>
<br>Question 3: Can those restraints be lambda (in alchemical free energy simulation) dependent?<br><br>You may have known what I'm trying to do: Change one molecule to dummy, so I need restrain it at dummy state while no restraint is wanted at real state.<br>
<br>Thanks,<br>Luke<br>
</blockquote></div><br>