Re: multiple dynamic sections in the config file?

From: Chris Harrison (
Date: Thu Aug 23 2012 - 22:55:50 CDT

This depends on the config option. At present rigidbonds cannot be
changes "on-the-fly." I would suggest setting up multiple namd config
files, then in your job submission script simply call namd twice.
Yes, the namd startup-time will be there, but unless you're doing many
short runs, this should work for you.

If there are specific config options that you'd like to be able to
change on-the-fly, please let us know.


On Thu, Aug 16, 2012 at 7:03 PM, Jacqueline Schmidt
<> wrote:
> Dear Namd users,
> I am a beginner in namd, so I apologize in advance if my question is so
> primitive. Is it possible to include a couple dynamic sections (equilibrium,
> production, etc) in one input file (with different settings such as rigid
> bonds and so on) the same way as for example in lammps? I know how to
> restart the simulation but I'd like the process to be a bit faster...
> Thanks
> Jakie

Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801       Voice: 773-570-6078                          Fax: 217-244-6078

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