Re: Supervised MD using NAMD

From: Seke Keretsu (
Date: Mon Jan 25 2021 - 07:39:55 CST

Hi Dr Eddie,

I was setting up my system for SUMD when this mail arrived.
This can be implemented within the namd configuration file. If you like I
can share the script with you. (Let me know which email)

Best Seke

On Mon, Jan 25, 2021 at 10:29 PM Dr. Eddie <> wrote:

> Hello all,
> I'd like to perform a supervised MD (SuMD) where basically I evaluate the
> distance of a ligand from its target every so often and reload a previous
> trajectory to continue if the new distance is larger or continue if the
> distance is smaller. I can kinda see how I can do this with a python script
> that writes the slurm/namd config file, but it would need mdtraj (or
> something similar) in order for me to be able to evaluate the distance I'm
> interested in. I don't know if that is common on Bridges and other XSEDE
> systems. The python script would need to sit in the queue with a dependency
> on the actual MD calculation each time. Is there a better way? Can the tcl
> config file handle full tcl commands (atomselect, distance etc) and
> conditionaly load other restore points?
> Much appreciated!
> Eddie

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:10 CST