Re: applying a force to some atoms

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Sun Jun 28 2015 - 15:54:42 CDT

http://lmgtfy.com/?q=namd+restraint+center+of+mass&l=1

Jerome

On 27 June 2015 at 13:22, jing liang <jingliang2015_at_gmail.com> wrote:

> Hi,
>
> I want to apply a force on certain atoms in my
> system.
>
> I wrote the following tcl lines within my namd input
> script:
>
> .... additional lines for the setup of namd
>
> dcdfreq 100
> xstFreq 100
> outputEnergies 100
>
> ################# TCL SCRIPT ############################
> tclForces on
> tclForcesScript {
>
> proc calcforces {} {
> loadcoords coords
> loadmasses masses
> print $coords(3433)
> }
>
> }
> #####################################################
> run 10000
>
>
> I saw that example in:
>
> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node33.html#SECTION00096800000000000000
>
> It should print the coordinates for the atom 3433 but instead it gives me
> some errors (below). Am I using the
> correct syntax for tcl? Actually, my goal is to apply a restraint force on
> the center of mass, is there
> some script available for that?
>
> Thanks.
>
> Errors I got:
>
> TCL: can't read "coords(3433)": no such variable
> FATAL ERROR: can't read "coords(3433)": no such variable
> while executing
> "print $coords(3433)"
> (procedure "calcforces" line 5)
> invoked from within
> "calcforces"
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: can't read "coords(3433)": no such variable
> while executing
> "print $coords(3433)"
> (procedure "calcforces" line 5)
> invoked from within
> "calcforces"
>
>
>
>
>
>
>
>

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