[gmx-users] Re: mass center of each molecule

[akn]

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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