[gmx-users] Getting nonbonded interactions from gmxdump

Ignacio Fernández Galván jellby at yahoo.com
Fri May 13 11:50:18 CEST 2011

Hi all,

I'm trying to extract the nonbonded interaction parameters for a whole system 
from the text dump generated by gmxdump (-s topol.tpr). I get it the relevant 
section is something like this:

functype[0]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06
functype[1]=LJ_SR, c6= 2.94705760e-03, c12= 4.75720708e-06
functype[2]=LJ_SR, c6= 5.42534457e-04, c12= 3.83789740e-07

All is fine with that, except that I see nowhere the correspondence between the 
"functypes" and the nonbonded pairs. In principle, I assume the first n^2 
functypes correspond to the interactions between the n atomtypes (7 in this 
case). But is there a guarantee that the nonbonded parameters are always listed 
first in the functypes (and, after them, there come the bonded parameters)?


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