[gmx-users] nonbond_params directive

[Eric Smoll]

Hi Justin,

No problem.  Thanks for the clarification.  I think I understand now.

Best,
Eric

On Sat, Jul 28, 2018 at 6:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
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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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>>>
> --
> ==================================================
>
> 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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