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

[gozde ergin]

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?

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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