Re: Switching PSF files during a run.

From: Joshua D. Moore (
Date: Tue Sep 11 2007 - 03:18:35 CDT

A NAMD person might be able to answer this better, but I don't think it
would be possible. NAMD seems to load the structure (definition of bonds,
angles, torsions, charges) at startup. So doing this internally in NAMD
seems impossible.

However, you could run this in a script (bash, csh, etc.)....your run script
for example whereby you restart NAMD after changing this parameter. Then
you could read in a different input file which has the new psf file.

So namd2 conf1.conf

then after changing

namd2 conf2.conf .....(which has the new psf file definition)

This wouldn't have anything to do with NAMD. It would just restart NAMD and
you would need to use the restart files (*restart.coor, *restart.vel, *
restart.xsc). The "parameter" would have to be something that is outside
NAMD, like a counter or something. I am not sure what you mean by

That's my idea..


On 9/7/07, Wang, Boyang <> wrote:
> Dear all,
> I have a quick question about running NAMD.
> We are trying to define a parameter during the simulation, and would like
> to switch the PSF file of the simulation when the parameter changes to
> some value.
> We would like to find a way that NAMD automatically changes its PSF file
> during one run, depending on the value of this parameter.
> So I wonder if there is any way of doing this by writing a script in the
> configuration file or else.
> Thanks a lot for your consideration.
> Boyang.

Joshua D. Moore
Graduate Student
North Carolina State University
Dept. of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC  27695-7905
Phone: (919) 513-2051
Fax:   (919) 513-2470

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