[gmx-users] 1,4 interactions
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 29 13:53:45 CEST 2010
Gavin Melaugh wrote:
> Hi all
>
> Can someone please get back to me on this. I have generated my own
> topology file from OPLS parameters by hand with the following format. I
> am now concerned that I haven't been calculating 1,4 interactions, which
> I thought were generated by setting gen-pairs = yes. I have read section
> 5 of the manual several times but am still unclear about this.
>
You can answer this question by analyzing your .edr file: are there LJ-14 and/or
Coul-14 terms? If so, then you're calculating 1-4 interactions. Seems to me
that, for OPLS, your approach is fine. It wasn't clear from your earlier posts
that you were using OPLS, hence the inability to know if what you were doing was
right or not. Different force fields have different underlying mechanics, so
the use of [nonbond_params] and/or [pairs]/[pairtypes] is somewhat dependent
upon your model.
-Justin
> Cheers
>
> Gavin
>
> parameter level
>> [defaults]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> 1 3 yes 0.5 0.5
>>
>> [atomtypes]
>> ;type mass charge ptype sigma(nm) epsilon(kjmol-1)
>>
>>
>> ;Molecular level
>> [moleculetype]
>> ; name nrexcl
>> tertpentane 3
>>
>>
>> [atoms]
>> ; atomnr type resnr residue name cgnr charge mass
>>
>>
>> [bonds]
>> ; ai aj func b0(nm) kb(kjmol-1 nm-2)
>>
>>
>> [angles]
>> ; ai aj ak func theta(deg) ktheta(kjmol-1 rad-2)
>>
>>
>> [dihedrals]
>>
>>
>> ;System level
>> [system]
>>
>>
>> [molecules]
>> ; moleculename number
>>
>>
>>
>>
>>
>>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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