[gmx-users] 1,4 interactions

[Gavin Melaugh]

A few points then,

1) So a [pairs] directive would include all the atom indices of the 1,4
interactions and the coressponding values of sigma and epsilon?, which I
would do manually.

2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions
which are not present in the pair list from normal LJ parameters using
Fudge LJ". Sorry if I am coming across stupid, but that seems different
to what you're saying?

3) Also am Icorrect about the normal nb-LJ coming from the [atom types
directive]

4) I suppose a very obvious question would be; What is the difference
between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc)

Gavin

P.S I appreciate you using your time to explain this
Justin A. Lemkul wrote:
>
>
> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>   
>>
>>
>