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

Justin Lemkul jalemkul at vt.edu
Thu Nov 16 21:50:38 CET 2017

On 11/16/17 3:45 PM, Srinivasa Ramisetti wrote:
> Exactly. I just wanted to know if we can get the order from the output information without calculating by hand as it is not always practical. Moreover, I am not sure if the order is preserved for each atom type. I will try this and let you know.

The matrix is probably just being established based on the order of 
parameters read. Do a simple test with 2 atom types, then 3, etc.


> Thank you,
> Srinivasa
> Sent from my iPhone
> On 16 Nov 2017, at 20:26, Wes Barnett <w.barnett at columbia.edu<mailto:w.barnett at columbia.edu>> wrote:
> On Thu, Nov 16, 2017 at 3:07 PM, Srinivasa Ramisetti <
> S.B.Ramisetti at leeds.ac.uk<mailto: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<mailto:w.barnett at columbia.edu>
> http://wbarnett.us
> --
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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