[gmx-users] look into tpr

[Valentin Gogonea]

Dear Gromacs users,

I am trying to get parameters for a new type of atom (sulfonium) and I 
want to make sure that all the parameters in the tpr are those I expect 
to be. So I used  gmxdump to get an ascii version of tpr. Here is an 
sample for ALA.tpr (dumped).

          LJ-14:
             nr: 30
             multinr[division over processors]: 30
             iatoms:
                0 type=49 (LJ14) 0 7
                1 type=49 (LJ14) 0 8
                2 type=50 (LJ14) 1 5
                3 type=50 (LJ14) 1 6
                4 type=50 (LJ14) 2 5
                5 type=50 (LJ14) 2 6
                6 type=50 (LJ14) 3 5
                7 type=50 (LJ14) 3 6
                8 type=51 (LJ14) 5 7
                9 type=51 (LJ14) 5 8
          Coulomb-14:
             nr: 0
          LJ (SR):
             nr: 0
          BuckingHam:
             nr: 0
          LJ (LR):
             nr: 0

My question is to what interactions correspond LJ (SR) and LJ (LR), I 
mean LJ interactions between which atoms.  How can I identify the atom 
types (their indices) that correspond to the following interaction types 
from 0-35 (in ALA)? Which is the relation between the functype index and 
the atom indices?


functype[0]=LJ, c6= 2.43619992e-03, c12= 1.69240002e-06
functype[1]=LJ, c6= 0.00000000e+00, c12= 0.00000000e+00
.
.
.
functype[34]=LJ, c6= 2.30061519e-03, c12= 1.58179989e-06
  functype[35]=LJ, c6= 2.26170011e-03, c12= 7.41579981e-07

Thank you.

Valentin