[gmx-users] Output center of mass of each molecules in a system.

[Christopher Neale]

make an index file with gmx make_ndx and then script it to create an index for each water molecule, e.g.:


gmx make_ndx -f my.gro -o index.ndx << EOF

$(for((i=1;i<=100;i++)); do echo r${i}; done)

q

EOF


then you can likewise script the input to gmx traj

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Li, Shi <sli259 at g.uky.edu>
Sent: 08 June 2017 11:26:46
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Output center of mass of each molecules in a system.

Dear GMX users,

I want to output the center of mass of each molecule in my simulation box.
I think I should use gmx traj, with -com option. But this only gave me the
center of mass for the whole system. If my system only contains 100 same
solvent molecules, is there a method to output the center of mass for each
individual molecule in the system?

Thank you for any help!
Shi
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