[gmx-users] 1-4 LJ interactions

[Justin Lemkul]

On 4/1/20 8:57 AM, Andrey Gurtovenko wrote:
> Dear Justin,
>
> thank you for the clarification.
>
> I think my confusion is in part due to the urea topology file
> used in the manual as an example, which does not contain
> the [pairs] section.

Urea is probably a poor example because it actually doesn't have 1-4 
interactions since the H atoms have no LJ. So any [pairs] that are 
defined will have all zero parameters.

-Justin

> with kind regards,
>
> Andrey
>
> On Wed, Apr 1, 2020 at 3:32 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 3/31/20 12:59 PM, Andrey Gurtovenko wrote:
>>> Dear All,
>>>
>>> Recently I realized that I don't fully understand what should be done
>>> in Gromacs to account for 1-4 LJ interactions.
>>>
>>> According to the manual:
>>>
>>> "gen-pairs is for pair generation. The default is ‘no’, i.e. get 1-4
>>> parameters from the pairtypes list. When parameters are not present in
>>> the list, stop with a fatal error. Setting ‘yes’ generates 1-4
>>> parameters that are not present in the pair list from normal
>>> Lennard-Jones parameters using fudgeLJ."
>>>
>>> http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html
>>>
>>> Therefore, I had an impression that to account for 1-4 interactions in
>>> some generic force-field, it is enough to
>>> set gen-pairs=yes.
>>>
>>> However, it turns out that this is not the case:
>>> in addition to gen-pairs=yes, one has to EXPLICITLY list pairs in the
>>> [pairs] section of the topology file of a system.
>>> Otherwise 1-4 interactions are NOT accounted for.
>>>
>>> Can someone comment on this?
>>> If I am right, maybe it is worth to clarify this point in the manual?
>> The language in the manual is correct, either pair *parameters* are
>> generated, or they are not. The topology is different from the
>> parameters; if *interactions* are not there, then nothing is done.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 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
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

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