[gmx-users] nonbond_params directive

[Justin Lemkul]

On 7/28/18 8:35 PM, Eric Smoll wrote:
> Justin,
>
> Thank you for the guidance.
>
> "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."
>
> But this would change the LJ interaction for 1-4 pairs and all other pairs
> that are not excluded, correct?  Consider a UA model of cyclooctane.  This
> has 1 atomtype.  If you specify LJ parameters for the CH2 group in the
> atomtypes directive, GROMACS will apply the unscaled LJ interactions for
> non-excluded pairs and the scaled LJ interactions for 1-4 pairs.
>
> Say you want to implement the same behavior with a nonbond_params
> directive.  Since the directive takes atomtypes, there is no way to specify
> and scale the 1-4 CH2-CH2 LJ interactions.
>
> Am I missing something?

No, I screwed up. Sorry about that. The contents of [nonbond_params] 
apply nonbonded interactions, but the 1-4 scaling (fudgeLJ) is applied 
in [pairtypes] (hence the interaction with "gen-pairs"). Pairs are 
considered a bonded interaction, so the two are separate.

-Justin

> Best,
> Eric
>
>
>
> 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.
>
>
> On Sat, Jul 28, 2018 at 6:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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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

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