[gmx-users] Harmonic distance restraint during simulation

[Xavier Periole]

On Sat, 06 Sep 2008 06:13:35 -0400
  "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> 
> 
> Manoj Kumar Singh wrote:
>>   What if I want to restrain distance between two different molecules. I
>> tried this and getting error. I looked at some previous posts and didn't
>> find any solution to this. Some of them say it is limitation of Gromacs.
>> 
> 
> Since distance restraints are added to the topology of one molecule, I 
>believe than can only be applied intramolecularly.
Justin is right, it has to be intramolecular, but you can merge the two
topologies in one and then add your distance restraint.
try: pdb2gmx -merge
> -Justin
> 
>>   Is there any way I can put distance restraint between atoms of two
>> different molecules?
>> 
>> Thanks in advance!
>> 
>> Manoj
>> 
>> 
>> Manoj Kumar Singh wrote:
>>> Hi,
>>>
>>> I want to put distance based restrain between few pairs of atoms during
>>> initial dynamics (along with Lincs on hbonds). I don't know how can I do
>>> this.
>>>
>> 
>> Section 4.3.4 of the manual is probably a good start.
>> 
>> -Justin
>> 
>>> I will highly appreciate any suggestion.
>>>
>>> Manoj
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>> 
>> --
>> ========================================
>> 
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> 
>> ========================================
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> 
>> 
>> 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
>or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-----------------------------------------------------
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------