Re: Multiple input and output files

From: Josh Vermaas (
Date: Wed Nov 05 2014 - 20:54:02 CST

Hi Debashis,

If I understand your question properly, this is more of a personal
organization question. If I have highly similar systems, I'll put the
psf file and the different starting pdbs in a "build" directory, place
sequential NAMD configuration files in the root directory of the
project, and use symlinks to place the files in the appropriate
directories. This lets me have a "system.psf" and a "system.pdb" in each
systematically named directory, which lets me use the same NAMD
configuration files (also symlinked) in every directory. If you prefer
to use the *exact* same configuration file for repeated runs, it is also
possible using tcl commands to set variables so that you can use an
identical NAMD configuration file for successive runs, but I find this
approach to be very easy to break if something unexpected happens during

In short, unless I am misunderstanding the question, there is not per se
a NAMD-specific way of doing what you want, but with a combination of a
scripting language (bash, tcl, etc.), you can figure something out.
What's wrong with just copying the file in several places?

-Josh Vermaas

On 11/5/14, 8:20 PM, Debashis Kundu wrote:
> Hello NAMD users,
> My name is Debashis. I am new to NAMD and this is my first mail. I am
> trying to run NPT of 4 configurations of a system. The configurations
> have same number of atoms. The topology and pdb files are in
> respective directories. I am trying to generate a single NPT script
> which will take input from each directory one after another and dump
> the output in respective directory. The simulation will run in series.
> I have tried to search suitable command in user guide but unable to
> find it. Please suggest me about the suitable commands for that.
> --
> ****************************************************
> *Thanks and Regards*/*,*
> /
> Debashis Kundu
> PhD student
> Drexel University
> Dept. of Chemical & Biological Engg.
> ***************************************************

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