[gmx-users] 1,4 interactions

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 29 15:59:56 CEST 2010

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]


> 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.


> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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