[gmx-users] wierd gro file output.

[Mark Abraham]

Hi,

What were the actual commands, e.g. to grompp and trjconv that produced
such results? I think you've done something mutually inconsistent.

Mark

On Mon, Apr 18, 2016 at 3:22 PM abhishek khetan <askhetan at gmail.com> wrote:

> 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
> --
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