[gmx-users] gmxdump output

Milton Taidi Sonoda msonoda at iqm.unicamp.br
Thu Jan 15 16:05:01 CET 2004

Hi all
More very simple questions.
1) I've performed

#gmxdump -s system.tpr | more

and in the meadle of the output there were
lots of

            functype[0]=LJ, c6= 2.03186437e-03, c12= 3.73510602e-06
            functype[1]=LJ, c6= 2.03186437e-03, c12= 3.73510602e-06
            functype[2]=LJ, c6= 2.03186437e-03, c12= 3.73510602e-06
            functype[3]=LJ, c6= 2.03186437e-03, c12= 3.73510602e-06
            functype[4]=LJ, c6= 5.43253613e-04, c12= 3.96031993e-07
            functype[5]=LJ, c6= 2.33295723e-03, c12= 3.06813695e-06
    and so on.
I would like to know how to identify to which pair of sites
are these LJ parameters related to.

2) Even ahead in the gmxdump output it has

               0 type=102 (CONSTR) 0 1
               1 type=103 (CONSTR) 21 22
               2 type=103 (CONSTR) 19 20
               3 type=103 (CONSTR) 17 18
               4 type=103 (CONSTR) 15 16
               5 type=103 (CONSTR) 13 14
               6 type=104 (CONSTR) 5 23
               7 type=105 (CONSTR) 5 12
               8 type=105 (CONSTR) 5 11
               9 type=104 (CONSTR) 4 21
    and so on ...
which I gess is related to constraints, been the
last two integers of each line 1rs and 2nd bonded neighbor.
Is it right?
However in my system.mdp file the constrains run parameters
are setted as.

             constraints    = none 
             unconstrained_start    =  yes  
Is it still right?

Thank you very much in advance,
Milton Taidi Sonoda

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