[gmx-users] force fileds gromos and oplsaa

Faezeh Pousaneh fpoosaneh at gmail.com
Thu Nov 16 14:45:09 CET 2017


Thanks a lot Justin!


Best regards


On Thu, Nov 16, 2017 at 2:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/16/17 8:28 AM, Faezeh Pousaneh wrote:
>
>> Hi
>>
>> sorry for silly question, but I did not find my answer by searching.
>>
>> In gromos force fields, the file nonbonded.itp includes nonbonded
>> parameters for two different atoms, e.g
>>
>> C O 1 2.300953E-03 2.222000E-06
>>
>> while I do not see oplsaa provides parameters for nonbonded interactions
>> of
>> different atoms, why?
>>
>
> The [nonbond_params] section specifies atom pairs for which normal
> combination rules do not apply, e.g. pair-specific Lennard-Jones parameters
> (CHARMM calls these NBFIX, for instance).
>
> Some force fields use them, others don't (and calculate everything via
> combination rules). In the case of OPLS-AA, there are a huge number of atom
> types, more than any other force field (AFAIK), which is essentially doing
> the same thing - there are highly specific parameter optimizations for
> given interactions.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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