[gmx-users] restraints between two different molecules
jalemkul at vt.edu
Fri May 27 17:12:21 CEST 2016
On 5/27/16 6:52 AM, Rebeca García Fandiño wrote:
> Thanks a lot for the suggestion, Mark.
> I have had a look at the documentation and I still have several doubts. I want to introduce distance restraints between an Ni2+ atom and two different ligands (so 3 molecules are implied).
> 1) I have understood that in the topology file I should include this section:
> [ intermolecular-interactions ]
> [ distance_restraints ]
> ; i j type label funct lo up1 up2 weight
> It is not clear to me what lo, up1, up2 mean. In the GROMACS
> manual it is said that they hold the values of r0, r1 and r2 from eqn.
> 4.83. If my restraint distance is 0.2 nm...which are the values of lo,
> up1 and up2 I should consider?
Depends on how tight you need the restraint. The restraint potential is
illustrated in Figure 4.15 of the manual. That might make it clearer.
> 2) I have read that I should also include some options in the .mdp file. disre = simple would it be enough? Or more options are needed?
> Thanks a lot for your help again.
> Best wishes,
>> From: mark.j.abraham at gmail.com
>> Date: Wed, 25 May 2016 14:19:26 +0000
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] restraints between two different molecules
>> On Wed, May 25, 2016 at 4:11 PM Rebeca García Fandiño <regafan at hotmail.com>
>>> Dear Gromacs users,
>>> I am trying to apply some distance restraints between two different
>>> molecules in a Gromacs simulation. I have read different things in the
>>> Gromacs list, such as both molecules should be in the same [atomtype]
>>> section (which is not the case)
>> In old versions, it is necessary to have such restraints within the same
>> moleculetype (not atomype, of course). This was because the system is built
>> from x copies of each moleculetype.
>> and also something related to the use of "pull_ngroups = 2". But it is not
>>> clear to me, and I don´t know how could I do it, even if this is possible.
>>> So, the question is...would it be possible to apply restraints between
>>> diferent molecules during a simulation?
>> GROMACS 5.1 introduces an [intermolecular_interactions] that precisely
>> addresses this issue without needing changes to [moleculetypes] or the use
>> of the pull code. Please see the documentaioin for details. :-)
>> Any help would be appreciated.
>>> Best wishes,
>>> Dr. Rebeca Garcia
>>> Santiago de Compostela University
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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