[gmx-users] 1,4 interactions

[Gavin Melaugh]

Hi Justin

I just wanted to say a big thanks for your time and patience

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> 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 ?
>>
>
> Yes.
>
>> 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?
>>
>
> Yes, in conjunction with FudgeLJ and FudgeQQ.
>
> -Justin
>
>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>   
>>>>
>>
>>
>