[gmx-users] the comm_mode

[OZGE ENGIN]

Hi Yang,

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 

Ozge

-----Original Message-----
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.
 
Regards,
Yang Ye



----- 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


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
　　　　　　　　

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Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China 

Tel:   +86-10-62773779(O) 
Email: li.dc06 at gmail.com
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