Setting constraints for SMD simulation

From: Charles Whidborne (
Date: Mon Sep 15 2014 - 20:20:39 CDT


I am wanting to perform an SMD simulation on a DNA system to pull off a
single strand from its complementary strand. I understand that in order to
allow the strand to be pulled off, the other strand needs to be constrained
so that it isn't pulled along with it. My initial thought was to just set
constraints [on] in the configuration file, however i am uncertain whether
this will constrain the atoms to the positions in which they were first
built (before minimisation and equilibration) or if NAMD will constrain
them to the position they ended up at at the end of the equilibration, from
which i am starting the SMD simulation from.

I am inclined to think NAMD will constrain them to the positions they were
originally 'built' to, thus leading to errors in the simulation and
possibly stopping the simulation from running (though i haven't tried
running it yet), if this is so, is it possible to export the final
positions of the equilibration to a separate pdb file which i can use to
define the constraint positions? or is NAMD able to constrain to the
positions at the end of the equilibration simulation?

This is the first time implementing SMD, so any further advice or
recommendations on how to do this would be appreciated.

Thanks in advance,


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