[gmx-users] the comm_mode

Yang Ye leafyoung at yahoo.com
Sun Oct 14 16:07:18 CEST 2007

----- Original Message ----
To: leafyoung at yahoo.com; gmx-users at gromacs.org
Cc: gmx-users at gromacs.org
Sent: Sunday, October 14, 2007 8:33:28 PM
Subject: Re: Re: [gmx-users] the comm_mode

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?

>> It is not because of this reason, it is due to PBC. Simulation in vacuum is usually done without PBC, Rotation is recommended.
>> COM velocity removal's effect is directly visible, so if "Linear" works for you, you may use it.

Thanks in advance 


-----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.

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,


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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