[gmx-users] 1,4 interactions

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Hi Justin
> 
> Thanks for replying. I have checked the energy file and there are no 1,4
> terms, which is what I expected. I should clarify that my parameters are
> taken from the OPLS ua forcefield but I have relabelled them for my own
> model, which is not a common molecule. Therefore all the info on the
> molecule is in .top and obviously the .gro file. i.e. there are no
> #include statements. Now I take it that the non-bonded LJ are taken from
> the [atom types] directive? The question is then how and where do I
> state the 1,4 terms. I always thought that when gen-pairs = yes, then
> gromacs would generate a list of all the 1,4 interaction types?
> 

You don't explicitly state 1-4 terms with OPLS-AA.  While you don't need a 
[pairtypes] directive, you do need a [pairs] directive to dictate the 1-4 
interactions.  Setting "gen-pairs = yes" generates the parameters, such that a 
[pairtypes] directive is unnecessary.

-Justin

> Gavin
> 
> Justin A. Lemkul wrote:
>>
>> 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

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