From: dhacademic (dhacademic_at_gmail.com)
Date: Mon Sep 06 2010 - 10:29:38 CDT
my version is NAMD 2.7b1
On Mon, Sep 6, 2010 at 11:14 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
> 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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