[gmx-users] nonbond_params directive

[Justin Lemkul]

On 7/28/18 7:19 PM, Eric Smoll wrote:
> 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

You simply supply whatever the LJ combination should be for the 1-4 
pair. If you want 0.5 times what is listed, change the values.

> impossible since this directive accepts atom types, not atom numbers.

In what instance do you want the same LJ pair to have different 
interactions? That would be a recipe for a totally non-transferable 
force field.

-Justin

>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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