RE: Steered dynamics

From: JC Gumbart (
Date: Sat Nov 12 2011 - 01:18:06 CST

It's probably because the distance reported in NAMD is that projected along
the vector specified by "SMDDir".



From: [] On Behalf
Of Jacopo Sgrignani
Sent: Friday, November 11, 2011 4:57 AM
Subject: namd-l: Steered dynamics


Dear All
I'm doing some constant velocity SMD simulations of the unbinding process
for a small molecule from a protein binding site.
Now I would like to plot the force as function of the distance from the
center of mass of the binding site.
However, considering the coordinates of the center of mass of the ligand
printed in the SMD lines of the output and the coordiante of the center of
of the bindig site calculated in the first snapshot I'm not able to obtain
the same distance that I can see in VMD.
Am I missing some important detail?

Thanks a lot


Jacopo Sgrignani PhD
CNR-IOM-Democritos National Simulation Center
c/o International School for Advanced Studies (SISSA/ISAS)
via Bonomea 265,

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