RE: COM position

From: Kamp, Marc vander (
Date: Tue Jul 06 2004 - 01:40:01 CDT

Hi Mauricio,
Did you also read this in the user guide:
COMmotion < allow center of mass motion? >

Acceptable Values: yes or no

Default Value: no

Description: Speci es whether or not motion of the center of mass of the entire system

is allowed. If this option is set to no, the initial velocities of the system will be adjusted to

remove center of mass motion of the system. Note that this does not preclude later centerof-

mass motion due to external forces such as random noise in Langevin dynamics, boundary

potentials, and harmonic restraints.

(p.46 in the pdf)



        -----Original Message-----
        From: on behalf of Mauricio Carrillo Tripp
        Sent: Mon 5-7-2004 21:47
        Subject: namd-l: COM position

        Hi all, I'm not sure this went through last time (I haven't got any
        replies) , so I'm sending it again with more coments...
        Is there a way to keep the system's center of mass position fixed at a
        certain point (e.g. origin) ?
        is there a command in NAMD to accomplish this or do I have to write a
        script? How do I do it?
        Reading the manual I found in section 6.7.3 and 6.7.6 (Options for
        restraints and Examples, Fixed restraints page 80) that I can do something
        urestrain {
          posi group {(*,*,*)} kf=20 ref=(0,0,0)
        I'm not sure about the *'s though, should I use {all} instead?
        Would this work?
        Afterall, all I want to do is to keep the COM from moving in the Z
        direction... it should be something quite simple, but I'm not sure
        how to do it.
        Thanks for any help
        Mauricio Carrillo Tripp
        Chemistry Department
        Wabash College

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