[gmx-users] 1,4 interactions

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Justin
> 
> One last question.What is the point of the [nonbond_params] directive if
> all your LJ parameters are already specified in [atomtypes]?, also

You can define non-standard parameters here.  Otherwise, the normal combination 
rules are used.  It seems like, at least in the cases of the Gromos force 
fields, some of the values provided are the normal values that would be 
calculated by the combination rules, so I don't see the point.  Maybe it's a 
relic of previous versions where the section was necessary.  Just a guess.

> [pairs_nb].

Never heard of this directive.  I see it in the manual, but I can't find it in 
any of the actual force field files.

> Surely it is not necessary to list all nb pairs?
> 

No.  If an interaction is based solely on the normal combination rules for a 
force field, those combination rules are applied, as stated in section 5.3.3 
(after equation 5.2).

-Justin

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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