Sorry, but I have to ask some more questions. I have just started to perform
simulations in vacuum. I can understand not using of PME in vacuum simulations;
however, I can not understand the sentence you wrote :
'rotation is recomended.' COM velocity removal's effect is directly visible.
Is it related to conservation of angular momentum?
Thank you very much!
Oz.
-----Original Message-----
From: Yang Ye <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Sun, 14 Oct 2007 07:07:18 -0700 (PDT)
Subject: Re: Re: [gmx-users] the comm_mode
----- Original Message ----
From: OZGE ENGIN <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]; gmx-users@gromacs.org
Cc: gmx-users@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
Ozge
-----Original Message-----
From: Yang Ye <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@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 <[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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