Dear Justin,
Thank you very much for your answer.
I specified each molecule individually in index file and I used trjconv -sep
command
to seperate the system each step (conf1.gro, conf2.gro, conf3.gro,
conf4.gro). Then
I used script that you suggested, it was as;
groups=`grep "^\[" index.ndx | wc -l`
for ((i=1; i<$groups; i++)); do echo $((i++)) $i | g_traj -s topol.tpr -f
conf$i.gro
-n index.ndx -ox coord.xvg -com; done
and I obtained the center of mass of each molecule at each step in seperate
files.
For example; if the system has 5 molecules and the run has 4 steps, I obtain
20
seperate files. However, I want to collect the center of mass of all
molecules
at all steps in only a file as following example;
step molecule index x y z
0 0 1.15126297 -0.83798647 0.58398923
0 1 0.68224833 0.74993176 1.84797615
0 2 2.97914942 0.11095256 2.61386881
0 3 4.65560905 -0.26363975 0.17970542
0 4 0.56267048 1.31953148 0.91372036
0 5 1.82333602 -1.24385819 1.63649468
1 0 1.15081591 -0.83159143 0.58321940
1 1 0.68357557 0.76482290 1.84911002
1 2 2.97913055 0.11320974 2.61105259
1 3 4.65727424 -0.26322810 0.17973330
1 4 0.56043944 1.32080373 0.90883115
1 5 1.82315477 -1.24656235 1.63910681
2 0 1.15238968 -0.82695173 0.58273344
2 1 0.68630303 0.77769022 1.85014673
2 2 2.97731032 0.11649037 2.61009124
2 3 4.65780877 -0.26399845 0.18205542
2 4 0.55785475 1.32480364 0.90410962
2 5 1.82237425 -1.25034522 1.64005468
3 0 1.15513001 -0.82180588 0.58414463
3 1 0.69432865 0.79014913 1.85176367
3 2 2.97255177 0.12185169 2.60981656
3 3 4.65625400 -0.26611685 0.18777379
3 4 0.55652912 1.33345131 0.89997690
3 5 1.82007758 -1.25560496 1.63930391
How can I do this by using shell script in gromacs?
Sincerely yours,
Akn.
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