Re: Spherical harmonic restraint

From: Morad Alawneh (alawneh_at_chem.byu.edu)
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:
keep_water_out.tcl

thanks



Morad Alawneh

Department of Chemistry and Biochemistry

C100 BNSN, BYU

Provo, UT 84602



Michael Grabe wrote:
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:


<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
that?</bigger></bigger></bigger></bold>


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




  

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