You didn't tell if you are using an absolute reference or not.
With an absolute reference you should not remove the com motion.
Berk.
From: "Zhou Bo" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: <[email protected]>
Subject: RE: [gmx-users] AFM Pulling and com motion
Date: Thu, 20 Sep 2007 22:44:29 +0800
Thanks to Berk. I just tested two system, one with stopcm and the other
without stopcm. I calculated the pull forces and compared them with each
other. There are really some distinct differences between them during the
80ps simulation. I worry about it, for example, in long time simulations,
so
I want to know which one is the better and reliable choice, stopcm or
without stopcm. As I know, the NAMD package only removes the initial center
of mass motion.
Thanks for your reply.
>>Hi GXM Users,
>> I'm trying to execute some AFM Pulling. I followed the pull code
tutorial
>>from GMX WORKSHOP 2007, and I found there is no specific to com motion
in
>>mdp, so the default is "comm-mode=Linear" and "comm-grps=System". I was
>>confused about it as I believed we should not stopcm when doing AFM
Pulling
>>because of the external force. Does it problematic to stopcm when doing
AFM
>>Pulling?
>>
>>Thanks!
>>
>This depends on what type of pulling you are doing.
>If you have an absolute reference you are right.
>But when you pull between two groups of atoms, there are no
>external forces, but internal forces between two groups.
>Berk.
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_________________________________________________________________
Talk with your online friends with Messenger
http://www.join.msn.com/messenger/overview
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
