Supervised MD using NAMD

From: Dr. Eddie (
Date: Mon Jan 25 2021 - 07:27:32 CST

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!

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