[gmx-users] the comm_mode
OZENGIN at KU.EDU.TR
Sun Oct 14 14:33:28 CEST 2007
I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations.
Is it due to the relatively rapid convergence of molecules in the vacuum environment?
Thanks in advance
From: Yang Ye <leafyoung at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Sun, 14 Oct 2007 03:42:12 -0700 (PDT)
Subject: Re: [gmx-users] the comm_mode
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.
----- Original Message ----
From: Dechang Li <li.dc06 at gmail.com>
To: gmx-users <gmx-users at gromacs.org>
Sent: Sunday, October 14, 2007 5:34:35 PM
Subject: [gmx-users] the comm_mode
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.
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Email: li.dc06 at gmail.com
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