[gmx-users] Getting nonbonded interactions from gmxdump

Mark Abraham mark.abraham at anu.edu.au
Fri May 13 11:58:13 CEST 2011

On 13/05/11, Ignacio Fernández Galván  <jellby at yahoo.com> wrote:
> 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:
> atnr=7
> ntypes=50
> 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)?

Probably - but the functype encodes the type. To be sure of what's going on you'd have to look at the grompp code that fills this data structure.

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