From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Sep 06 2010 - 10:14:25 CDT
Hi,
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
> user-manual.
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
> segments
> (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.
Cheers,
Jerome
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