From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Mon Sep 06 2010 - 14:10:06 CDT
It would be best to use 2.7b2 or 2.7b3, in general.
In the specific example, you used four psfSegID values but you specified
them separately: the correct syntax is to put them on the same line (one
psfSegID keyword with multiple values).
Also, there may be only one atomNameResidueRange option for each psfSegID
value, not two of them as in your case. You should use something like
"psfSegID A A B B C C D D" to fix this.
Dr. Giacomo Fiorin
ICMS - Institute for Computational Molecular Science - Temple University
1900 N 12 th Street, Philadelphia, PA 19122
On Mon, Sep 6, 2010 at 11:29 AM, dhacademic <dhacademic_at_gmail.com> wrote:
> my version is NAMD 2.7b1
> On Mon, Sep 6, 2010 at 11:14 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
>> 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
>> > 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).
>> > 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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