From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Sep 06 2010 - 10:14:25 CDT
First, for TMD, you probably need the restraint force, so you should
request outputAppliedForce, not outputSystemForce.
> (1) Do the "centers" and "targets" keywords mean the initial and final RMSD
> of the system? I feel confused by reading the related part of the
They are the initial and final values of the center of the restraint
potential. If all goes well, the RMSD should follow.
> (2) I want to define 4 (segments) * 236 (per segment) = 944 atoms in the
> input. However, only 237 atoms are defined according to the output
> file. Someone else used a similar way to define atoms within different
> (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/12359.html). What
> is wrong with my syntax?
Not sure. What version of NAMD are you using? I wonder if this could
be an old bug that is now fixed.
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