I'm not sure that I interpret your question correctly, but my guess
is that you want to remove the center-of-mass translation and/or
rotation. You can set this in the .mdp file with the commands
comm_mode and comm_grps and an appropriate index file.
Please refer to the manual or the online mdp option reference for the
details:
http://www.gromacs.org/documentation/reference/online/mdp_opt.html
- Daniel
On Apr 16, 2008, at 16:26, tuyusong wrote:
Hi, all,
I have a system with one carbon Nanotube and lots of
water, in which Nanotube is frozen. How do I remove the center-of-
mass:
1) only remove the COM of SOL
2) remove both COM of SOL and CNT, separately
3) only remove the COM of "system" as a whole.
4) do not use any COM
How do I make the choices?
I use gromacs program 3.3.3
Thank you very much!!!
Yusong.
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---
Daniel Larsson
Molecular Biophysics group
Department of Cell and Molecular Biology
Uppsala University
+46-18-471 4006 (phone)
+46-18-511 755 (fax)
http://xray.bmc.uu.se/~larsson
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