[gmx-users] obtaining .gro timeframe

[Chetan Mahajan]

Dear All,

I need some help to generate .gro file corresponding to a given timeframe
of the trajectory obtained in gromacs MD run.

Currently, I am using following command to generate a .gro timeframe (5000
ps) from .xtc trajectory:


*trjconv -f lnanop.xtc -o time5000.gro -s lnanop.tpr -dump 5000*

where lnanop.tpr is generated by following command at the beginning of the
MD run which geenrates above .xtc file:

grompp -f $sethome/prod_lnanopff16.mdp -c $b4prod/lnanop.gro -p
$sethome/outff18-2_aftermin.top -o lnanop.tpr -n $sethome/index18-2.ndx

where each file means by what is implied by its extension.

Now, the comparison of input file to grompp and time0.gro (initial)
timeframe generated by "trjconv" command on .xtc looks good. However, there
are some differences between the files lnanop.gro (generated at the end of
the gromacs MD run) and that generated from "trjconv" command to extract
last timeframe of the same xtc trajectory, *although files match on many
other accounts. Some of the output of -diff command on two files in the
following*:

@@ -2322,8 +2322,8 @@
    55SOL    HW1 2320   3.174   0.144   7.460
    55SOL    HW2 2321   3.041   0.201   7.382
    56SOL     OW 2322   0.015   1.114   1.210
*-   56SOL    HW1 2323  -0.031   1.076   1.130 *
*-   56SOL    HW2 2324  -0.040   1.096   1.292 *
*+   56SOL    HW1 2323   3.191   1.076   1.130*
*+   56SOL    HW2 2324   3.182   1.096   1.292*
    57SOL     OW 2325   1.398   3.388  10.246
    57SOL    HW1 2326   1.471   3.321  10.236
    57SOL    HW2 2327   1.365   3.388  10.341

- : for .gro file at the end of gromacs MD run
+ : for .gro timeframe file obtained from .xtc trajectory ( using trjconv):
that with no signs, is the common part of the two files

What's happening? Please comment. Thanks a lot!

regards
Chetan