[gmx-users] 1,4 interactions

[Justin A. Lemkul]

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
>>
>>
>>
>>
>>
>>   
> 

-- 
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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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