Re: Spherical harmonic restraint

From: Morad Alawneh (
Date: Thu Mar 02 2006 - 13:25:39 CST

Hi Michael,

Thanks for your advice.

Is the attached script the one that you mentioned?

Its name:


Morad Alawneh

Department of Chemistry and Biochemistry


Provo, UT 84602

Michael Grabe wrote:

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.


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

<excerpt><bold><bigger><bigger><bigger>Dear everyone,</bigger></bigger></bigger></bold>

<bold><bigger><bigger><bigger> 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.</bigger></bigger></bigger></bold>

<bold><bigger><bigger><bigger> Does anyone have any idea how to do

<bold><bigger><bigger><bigger> Thanks</bigger></bigger></bigger></bold>


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