[gmx-users] wierd gro file output.

[abhishek khetan]

Dear gmx-users,

I was analysing some trajectory files from a box of acetonitrile solvents
when i realised that despite using trjconv -pbc whole and then trjconv -pbc
no jump, the molecules appeared to be broken when visualising using pymol.

When i looked that the gro file, the final gro file was of the kind:

ACN216
 1296
    1ACN     C1    1   0.030   0.065   2.621
    2ACN     H2    2   0.110   0.009   2.572
    3ACN     H3    3  -0.006   0.008   2.706
    4ACN     H4    4  -0.052   0.080   2.550
    5ACN     C5    5   0.080   0.195   2.666
    6ACN     N6    6   0.120   0.298   2.702
    1ACN     C1    7   1.963   1.695   0.110
    2ACN     H2    8   2.012   1.649   0.196
    3ACN     H3    9   1.866   1.647   0.095
    4ACN     H4   10   2.024   1.681   0.021
    5ACN     C5   11   1.944   1.838   0.136
    6ACN     N6   12   1.928   1.951   0.157
    1ACN     C1   13   0.033   2.237   2.583
    2ACN     H2   14   0.129   2.281   2.609
    3ACN     H3   15  -0.009   2.290   2.497
    4ACN     H4   16  -0.035   2.247   2.667
    --------     ----
    --------     ----

Where as the input file at the beginning of the simulations had the form

GROup of MAchos and Cynical Suckers
 1296
    1ACN     C1    1   0.000  -0.117   0.000
    1ACN     H2    2   0.102  -0.154   0.000
    1ACN     H3    3  -0.051  -0.154   0.089
    1ACN     H4    4  -0.051  -0.154  -0.089
    1ACN     C5    5   0.000   0.028   0.000
    1ACN     N6    6   0.000   0.143   0.000
    2ACN     C1    7   2.050   1.716   0.214
    2ACN     H2    8   2.149   1.683   0.242
    2ACN     H3    9   1.984   1.707   0.300
    2ACN     H4   10   2.012   1.653   0.134
    2ACN     C5   11   2.054   1.855   0.169
    2ACN     N6   12   2.058   1.964   0.135
    3ACN     C1   13   2.580   2.268   2.635
    3ACN     H2   14   2.667   2.329   2.609
    3ACN     H3   15   2.506   2.278   2.557
    3ACN     H4   16   2.539   2.304   2.729

As you can see the output gro file has teh residue numbeing gobbled up,
although in a very orderly manner. Could you please suggest whats going on.
I was hoping that using -pbc whole would not make any difference because
none of the bond would be broken in my simulations. However, even after
using -pbc whole in the trjconv routine, I find molecules broken

Thanks for the help in advance.

-- 
MfG,
abhishek