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

Mark Abraham mark.j.abraham at gmail.com
Mon Dec 10 11:51:13 CET 2012

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


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
> --
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> Physical Chemistry
> Universidad de Murcia
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