RE: COM position

From: Mauricio Carrillo Tripp (trippm_at_wabash.edu)
Date: Tue Jul 06 2004 - 10:45:53 CDT

Hi Marc, thanks for the reply

I was aware of the COMmotion command, but this will only affect the initial
step. What I need to do is to allways keep it in the same position. I was
using
Langevin for temperature control but this would make the COM move a lot,
so I changed to Vel. Reassigment but it's still moving (not as much as before
though), but because of the analisys I want to make I need it to be still.
Do you
know if there's an easy way to do this?

Kamp, Marc vander said:
> 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
>
>
>
>

-- 
--------------------------------------------------
Mauricio Carrillo Tripp
Chemistry Department
Wabash College
http://chem.acad.wabash.edu/~trippm

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