[gmx-users] 1,4 interactions

[Gavin Melaugh]

Justin

One last question.What is the point of the [nonbond_params] directive if
all your LJ parameters are already specified in [atomtypes]?, also
[pairs_nb].
Surely it is not necessary to list all nb pairs?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> I just wanted to say a big thanks for your time and patience
>>
>
> No problem.  This exchange has made me realize that what's in the
> manual, while complete, lacks a bit of clarity.  I'm going to make
> some updates to the documentation for a future release.  Hopefully
> this will clarify some issues.
>
> -Justin
>
>> 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
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>   
>>>>
>>
>>
>