[gmx-users] atom types

Mark Abraham mark.abraham at anu.edu.au
Tue Aug 2 13:41:29 CEST 2011

On 02/08/11, Gavin Melaugh  <gmelaugh01 at qub.ac.uk> wrote:
> Hi Mark
> Thanks for the reply.
> I am currently reading that section of the manual and, unless I am
> completely mistaken, it seems to vindicate what I am saying.
> "Extra Lennard-Jones and electrostatic interactions between pairs of
> atoms in a molecule can be added in the [pairs] section of a molecule
> definition".
> In my [atom types] directive I have atomtype, charge mass, sigma and
> epsilon etc. All nonbonding parameters are then calculated according to
> the combination rule (in my case 3). 1-4 interactions are then
> calculated based on the information in [pairs] directive (all atoms are
> three bond away). I just have the atom indices of each pair in this
> directive therefore with gen_pairs = yes, the interaction parameters
> between each pair (which are 1-4) are calculated based on Fudge LJ and
> Fudge QQ (which are both 0.5 in my case). All of this in conjunction
> with nrexcl =3.

That will generate parameters for the interactions listed in [pairs] that do not have corresponding [pairtypes]. FudgeLJ and [nonbond_params] are used in such generation, per other parts of 5.7.

>   Or am I completely wrong?
> In my set up then, are 1-4 Coulombic interactions determined by the pair
> list and fudge QQ?

If the contradiction you think exists is this one...

> > On 02/08/11, *Gavin Melaugh * <gmelaugh01 at qub.ac.uk> wrote:
> >> Hi Justin
> >>
> >> Again thanks for the reply. I am not disagreeing with you but If I don't
> >> include a [pairs] directive in the topology file (with gen_pairs =yes),
> >> then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log
> >> file. When I include the [pair s] directive then both types of
> >> interaction are written to the log file. Therefore does gen_pairs= yes +
> >> [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ
> >> and QQ?

... then 5.3.4 indicates that the presence of a [pairs] directive will generate the 1,4 output fields. The parameters for that output are taken from [pairtypes]. If gen-pairs=yes then the parameters are generated, else some warning/error occurs. The example in 5.7.1 has some more explanation about the use of the fudge parameters.

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