Generally, linear. For simulation in vacumm, you need rotation.
With big molecules, equilibration may not be done thoroughly; this may result
in very obivious rotation that Linear can not prevent. So visualize your
trajectory and check your molecule. If it happens, you need to apply Rotation
in the beginning of your simulation for a few ns.
Regards,
Yang Ye
----- Original Message ----
From: Dechang Li <[EMAIL PROTECTED]>
To: gmx-users <gmx-users@gromacs.org>
Sent: Sunday, October 14, 2007 5:34:35 PM
Subject: [gmx-users] the comm_mode
Dear all,
There are three options of comm_mode: Linear, Angular and none.
The option Angular is said that "Remove center of mass translation
and rotation around the center of mass". Does it mean the option
Angular remove the translation and rotation BOTH ?
If I want to do a simulation such as a protein in the explicit
water, which option would be better? Or it will be the same?
Thank you for your reply.
Best regards,
2007-10-14
=========================================
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China
Tel: +86-10-62773779(O)
Email: [EMAIL PROTECTED]
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