[gmx-users] how to make choices of COM in the system with freeze group?

[Daniel Larsson]

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
larsson at xray.bmc.uu.se