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

[gozde ergin]

However in the paper they have mentioned that they increased the sigma  for amino nitrogen–carboxylate oxygen interactions 
by 0.13Angstrom   relative to the original value.
So I assume there should be original value? 
However you mentioned that there is no pair-specific LJ interaction in OPLSAA. 
Even if I add a [nonbond_params] what epsilon and sigma should I use? Because they talk about the increment in sigma and I do not know the original value.
Maybe I should connect them directly.

Thanks Justin.

> On 21 Jun 2017, at 16:46, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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
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> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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