From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
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)
Marc
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu on behalf of Mauricio Carrillo Tripp
Sent: Mon 5-7-2004 21:47
To: namd-l_at_ks.uiuc.edu
Cc:
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
conformational
restraints and Examples, Fixed restraints page 80) that I can do something
like
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
http://chem.acad.wabash.edu/~trippm
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