[gmx-users] restraints between two different molecules

[Justin Lemkul]

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.

-Justin

>
>
> 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,
>
> Rebeca.
>
>
>
>
>
>
>> 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
>>
>> Hi,
>>
>> On Wed, May 25, 2016 at 4:11 PM Rebeca García Fandiño <regafan at hotmail.com>
>> wrote:
>>
>>> 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. :-)
>>
>> Mark
>>
>> Any help would be appreciated.
>>> Best wishes,
>>>
>>> Dr. Rebeca Garcia
>>> Santiago de Compostela University
>>> Spain
>>>
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>  		 	   		
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================