[gmx-users] 1,4 interactions

[Gavin Melaugh]

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?

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