Re: Spherical harmonic restraint

From: Michael Grabe (Michael.Grabe_at_ucsf.edu)
Date: Thu Mar 02 2006 - 13:19:53 CST

Morad,

you will have to use a tcl script that follows the ions
and applies forces to them if they get close to the
area that you are interested in.

i think that there is a template script somewhere on the
NAMD website which does this for water molecules
in the membrane interface.

if you can't find it, i will send you a script.

-michael

On Mar 2, 2006, at 9:39 AM, Morad Alawneh wrote:

> Dear everyone,
>
> I would like to use excluded spherical harmonic restraint in
> restraining number of ions to be a way from this sphere through
> umbrella sampling simulation, the only thing I found in the manual is
> Spherical Periodic Boundary, which is not helpful.
>
> Does anyone have any idea how to do that?
>
> Thanks
>
>
>
> --
>
>
> Morad Alawneh
> Department of Chemistry and Biochemistry
> C100 BNSN, BYU
> Provo, UT 84602
>
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