[gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Justin Lemkul]

On 6/21/17 10:39 AM, gozde ergin wrote:
> Hi MArk,
> 
> Thanks for the respond. I understood that point however I still do not get which sigma to change.
> I the paper JCTC 2017, Miller et. al. they have mentioned that they increase the for nitrogen–carboxylate oxygen interactions in OPLSAA.
> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino notrogen and one for carboxylate oxygen.
> 
>                                                                                sigma            epsilon
>   opls_287   N3   7  14.00670    -0.300       A    3.25000e-01  7.11280e-01
>   opls_272   O2   8  15.99940    -0.800       A    2.96000e-01  8.78640e-01
> 
> Which one defines the amino nitrogen–carboxylate oxygen interactions?
> Which sigma should I change?
> 

What people are doing more and more is introducing pair-specific parameters to 
override the combination rule values.  That's likely what is being referred to. 
OPLS-AA by default does not use pair-specific LJ interactions, hence why you 
find no [nonbond_params] in ffnonbonded.itp.  The same is true of AMBER.  CHARMM 
uses some (also called NBFIX in the literature), while GROMOS uses a ton of these.

To override the LJ combination rules, add a [nonbond_params] directive with the 
published parameters, which refer to an *interaction*, not an atom type.

-Justin

> Thanks
>> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>
>> Hi,
>>
>> Different force fields work differently and thus are implemented
>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
>> is a property of the atomtype
>>
>> Mark
>>
>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeergin at gmail.com> wrote:
>>
>>> Dear users,
>>>
>>> I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
>>> interactions in OPLSAA in GROMACS.
>>> However I have difficulties to understand which parameter i should change
>>> in ffnonbonded.itp file?
>>> I am looking something like [ nonbond_params ] section however it is not
>>> exist in ffnonbonded.itp?
>>> Any help would be appreciated.
>>>
>>> Thanks in advance.
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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

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