Targeted and Steered MD: Why must the initial and targeted PDBs have identical # of atoms?

From: Bryan Roessler (
Date: Mon Aug 26 2013 - 11:24:31 CDT


This is a limitation that has been hindering me for some time. Running
targeted or steered MD on a protein in explicit solvent is quite difficult
because both the initial and targeted PDBs must contain the same number of
atoms. When the protein is in different conformations, random distribution
of solvent usually results in a different number of atoms between the two
systems, causing NAMD to complain, even though I am only targeting atoms
within the protein. I have been manually removing water molecules from the
corners of the solvation box in order for the numbers to match but this can
still be problematic due to having to regenerate the PSF. Is there an easy
workaround for this? Could TMD and SMD in NAMD be implemented such that
only atoms selected for targeting using occupancy values are considered in
the comparison?


Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
Knowledge that will change your world

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