[gmx-users] What is the purpose of the [ pairs ] section?

[Mark Abraham]

Also, building yourself a test system of (for example) a single amino acid,
varying the .top settings, compiling a .tpr and using mdrun -rerun to
investigate the effects can be a good way to acquire confidence that the
physics you are implementing does match the model you intend.

Mark

On Mon, Dec 10, 2012 at 11:51 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Indeed, thanks Javier.
>
> These kinds of features are a bit awkward to document because there are
> lots of conditions under which various forms of interaction generation are
> used - primarily varying with the forcefield. Different force fields
> motivate various capabilities of pdb2gmx and it's not fully appropriate to
> describe the capabilities without reference to any force fields, nor to
> describe only the capabilities relevant to each force field in turn.
>
> AFAIK section 5.7.1 of the manual has the required information, but some
> of it is buried in the explanation of the worked example. Also, do check
> out the 4.6-beta1 manual http://www.gromacs.org/Documentation/Manual,
> because the tables in 5.7.1 now have cross references to sections (such as
> 5.3.4) to help find the necessary information.
>
> If there's something really missing, do let me know (e.g. via
> http://redmine.gromacs.org/projects/documentation).
>
> Mark
>
>
> On Mon, Dec 10, 2012 at 10:35 AM, Javier Cerezo <jcb1 at um.es> wrote:
>
>> Hi
>>
>> The pair section specifies the atoms between which a non-bonded
>> interaction will be build up, even if the "normal" non-bonded is excluded,
>> what is a mechanism to build 1-4 interactions. So, if you want a 1-4
>> interaction to be taken into account, you need to specify it in the
>> topology, in the same way you need to include all bonds, angles...
>>
>> VdW pair interactions should be listed in ffnonbonded.itp, under [
>> pairtypes ] directive, where grompp can find them. However, if such
>> interactions are not there, it is still possible to automatically generate
>> them in the same way as "normal" VdW are generated, and additionally
>> scaling by fudgeLJ. For such pair generation, gen-pairs should be set to
>> yes in [ defaults ], otherwise grompp will give an error if it does not
>> find them in ffnonbonded.itp. Note that if pairs are deffined in
>> ffnonbonded.itp and you set gen-pairs to yes, they will be taken from
>> ffnonbonded.itp.
>>
>> As for coulomb pair interactions, they will be generated only through
>> gen-pairs=yes, as (there is not any directive for them in ffnonbonded.itp),
>> simply scaling the "normal" coulomb by fudgeQQ.
>>
>> So, in the case of OPLS, the resulting 1-4 interactions, providing the [
>> defaults ] that are in forcefield.itp and the fact that there is not [
>> pairtypes ] for this force field, will be those prescribed for the force
>> field, but only if you include the appropriate line under [ pairs ] for all
>> possible combinations.
>>
>> Javier
>>
>> El 08/12/12 23:12, Andrew DeYoung escribió:
>>
>>  Hi,
>>>
>>> I am sure that this is a rather basic question, but I am wondering if you
>>> can please help me to understand something described in the manual.
>>>
>>> What is the purpose of the [ pairs ] section of an .itp file?  What
>>> information does it contain?
>>>
>>> Section 5.3.4 (page 112) of the version 4.5.4 manual says:
>>>
>>> "Extra Lennard-Jones and electrostatic interactions between pairs of
>>> atoms
>>> in a molecule can be added in the [ pairs ] section of a molecule
>>> definition. The parameters for these interactions can be set
>>> independently
>>> from the non-bonded interaction parameters. In the GROMOS force fields,
>>> pairs are only used to modify the 1-4 interactions (interactions of atoms
>>> separated by three bonds). In these force fields the 1-4 interactions are
>>> excluded from the non-bonded interactions (see sec. 5.4)."
>>>
>>> However, I am using the OPLS force field, not GROMOS.  OPLS prescribes
>>> that
>>> 1-4 nonbonded interactions are to be taken at half strength (i.e.,
>>> fudgeQQ =
>>> 0.5 and fudgeLJ = 0.5).  Does this mean that I should specify all
>>> possible
>>> 1-4 nonbonded interactions in the [ pairs ] section?  If I have nrexcl =
>>> 3
>>> specified in [ moleculetype ], then can I assume that 1-5, 1-6, 1-7, etc,
>>> interactions will be taken into account (at full strength), even if such
>>> pairs are not specified in [ pairs ]?  I have set gen-pairs = yes,
>>> fudgeLJ =
>>> 0.5, and fudgeQQ = 0.5.
>>>
>>> Thank you for your time!
>>>
>>> Andrew DeYoung
>>> Carnegie Mellon University
>>>
>>>
>> --
>> Javier CEREZO BASTIDA
>> Ph.D. Student
>> Physical Chemistry
>> Universidad de Murcia
>> 30100, Murcia (SPAIN)
>> T: (0034)868887434
>>
>>
>> --
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