[gmx-users] 1,4 interactions

[Gavin Melaugh]

Right, I think the penny has finally dropped. On the back of what you said.

1)In my topologies I have always listed say a [bond] directive, with
bond indices,function, k, and r0. I could however just list the indices
and the function, and then have the corresponding parameters in the
[bond types] directive, which save me associating the parameters to each
individual bond ?

2) In reponse to what yo said finally "If you list specific pairs of
atoms in a [pairs] directive, then grompp will search for the
appropriate parameters listed in a [pairstypes] directive.  If none are
found, and "gen-pairs = yes," grompp generates the appropriate
parameters for you." Are the parameters generated from the [atomtypes]
directive?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> 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.
>>
>
> No.  A [pairs] directive simply lists the pairs of atoms for which 1,4
> interactions should be calculated.  No parameters are listed here. 
> Format:
>
> atom_i atom_j func_type
>
>> 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?
>>
>
> Not at all.  The parameters for a specific interaction are given in a
> [pairtypes] directive.  If these parameters are not present and
> "gen-pairs = yes" then they are calculated.  If parameters for a
> specific pair are not present, and "gen-pairs = no" then grompp
> generates a fatal error.
>
>> 3) Also am Icorrect about the normal nb-LJ coming from the [atom types
>> directive]
>>
>
> Yes.
>
>> 4) I suppose a very obvious question would be; What is the difference
>> between a [pairtypes] directive and [pairs] directive (bonds,
>> bondtypes etc)
>>
>
> A [*type] directive lists the parameters that should be a applied to
> whatever interaction type might be found.  For instance, a [bondtypes]
> directive contains default parameters for all the bonds you might
> find, like C-C.  If you then have a [bonds] directive that lists:
>
> ; ai  aj  func
>    1   2    1
>
> ...and atoms 1 and 2 are both C, then grompp finds the corresponding
> parameters in the [bondtypes] directive and applies them to that bond,
> a process which it carries out for all the rest of the interaction
> types, including pairs.  If you list specific pairs of atoms in a
> [pairs] directive, then grompp will search for the appropriate
> parameters listed in a [pairstypes] directive.  If none are found, and
> "gen-pairs = yes," grompp generates the appropriate parameters for you.
>
> -Justin
>
>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>   
>>>>
>>
>>
>