On 13/05/11, Ignacio Fernández Galván <[email protected]> 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. Mark
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