RE: NAMD-L: question about harmonic constraints

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Apr 10 2006 - 00:49:47 CDT

I'm almost positive that forces applied to the group are applied to the
center of mass, which has to then be distributed to each atom appropriately,
so it should be okay for your purpose.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Margaret Shun Cheung
Sent: Saturday, April 08, 2006 10:30 PM
To: JC Gumbart
Cc: namd-l_at_ks.uiuc.edu
Subject: RE: namd-l: NAMD-L: question about harmonic constraints

Dear JC and NAMD users,
Thank you for the info. I checked tclForces on the manual and saw the
option of "addgroup". I am confused with its description "...Aggregate
forces may then be applied to the group as whole."..

Assuming that my system is not a rigid body, I wonder whether the
description refers to the force acting to the center of mass or acting
to each atom in the group.
Thank you very much.
Sincerely,
Margaret

On Sat, 8 Apr 2006, JC Gumbart wrote:

> It is possible to use SMD with a velocity of zero to restrain the center
of
> mass of atoms along one axis. However, if you try to restrain along more
> than one axis, very interesting problems will arise.
>
> Unfortunately, for anything more, I believe scripting with tclForces may
be
> the only option.
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> Of Margaret Shun Cheung
> Sent: Saturday, April 08, 2006 1:34 PM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: NAMD-L: question about harmonic constraints
>
> Dear NAMD users,
>
> I looked up the user guide for harmonic constraints and the option is that
> each assigned atom is referenced to a specific coordinate in the
> "consref <file>". What should I do if I want to impose harmonic
> constraints to
> the center of mass of several atoms during the simulations instead (like
> what SMD does to the selected SMD atoms)? I looked up selectcontrX{Y,Z}
> too, but probably it's not what I was thinking for.
>
> Please share me with your insights!
> Thank you very much!
> Sincerely,
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------
>
>

Margaret S. Cheung,
Ph. D. Postdoctoral Fellow,

------------------------------------------------------------
Room 2117 Tel: (301) 405-4892
Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
University of Maryland http://glue.umd.edu/~mscheung
College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
------------------------------------------------------------

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