From: JC Gumbart (gumbart_at_ks.uiuc.edu)
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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Jacopo Sgrignani
Sent: Friday, November 11, 2011 4:57 AM
Subject: namd-l: Steered dynamics
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, 34136 Trieste Italy email: sgrigna_at_sissa.it
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