[gmx-users] how to output intramolecular pair interaction parameters

Wes Barnett w.barnett at columbia.edu
Thu Nov 16 21:25:14 CET 2017

On Thu, Nov 16, 2017 at 3:07 PM, Srinivasa Ramisetti <
S.B.Ramisetti at leeds.ac.uk> wrote:

> This is continuation to my previous question. I used gmx dump to output
> the 1-4 intramolecular interaction parameters. I could get the c6 and c12
> values for all the list of 1-4 pair nteractions within my top file.
> However, I could not understand the following lines in the output
> information under the ffparams starting from functype[0] to functype[63]. I
> do not understand how these 64 of c6,c12 values are related to 36 atoms (8
> atom types) that belong to my System. Could anyone explain me how can I
> know which functype belongs to a particular atom/atom type?

You have 8 atomtypes, which means 8 sigmas and 8 epsilons . Here it is just
iterating through those atomtypes, combining the sigmas and epsilons
according to the combination rule in your force field, and then calculating
and storing c6 and c12 in memory (8x8=64). I'm not sure what order it
processes things in though. Try doing some of the combining by hand and see
what matches up.

James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu

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