RE: NAMD-L: question about harmonic constraints

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Sat Apr 08 2006 - 22:30:13 CDT

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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