[gmx-users] nonbond_params directive

[Eric Smoll]

On Sat, Jul 28, 2018 at 2:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/26/18 5:52 PM, Eric Smoll wrote:
>
>> Hello GROMACS users,
>>
>> I have a quick question about the nonbond_params directive.
>>
>> If I provide gen-pairs=yes and fudgeQQ=0.5 in the defaults directive,
>> GROMACS will
>>
>
> That's fudgeLJ, not fudgeQQ, but yes.
>
> (1) compute VDW parameters for all atomtype-pairs and
>> (2) scale all 1-4 interactions specified in the pairs directive by 0.5.
>> Note that the parameters for the 1-4 interactions are obtained from (1).
>>
>
> Correct.
>
>
>> Will GROMACS still scale all 1-4 interactions by 0.5 if I specify VDW
>> parameters for all atomtype-pairs in a nonbond_params directive?
>>
>
> No. [nonbond_params] takes precedence. For any missing pair, and with
> gen-pairs = yes, fudgeLJ is used. It is not used for anything else.
>


Thanks for the reply.  That is dissapointing.  Then how does one implement
scaled 1-4 interactions with the nonbond_params directive?  It seems
impossible since this directive accepts atom types, not atom numbers.


>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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