[gmx-users] nonbond_params directive

[Eric Smoll]

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?

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
>
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