From: Axel Kohlmeyer (
Date: Tue Mar 16 2010 - 06:59:05 CDT


how should anybody be able to help you without
actually seeing the script that you are using or in
any other way be able to see what you are seeing?
there are a gazillion ways to write a NAMD input script,
almost as many as there are NAMD users.


On Tue, Mar 16, 2010 at 6:19 AM, Daniel Hornburg <> wrote:
> Hello,
> I am using NAMD for md and I am relativly new. I have a question concerning
> my equilibrium script. When I am watching the resulting trajectory in VMD
> (there is no error or something like that produced, all seems to be fine)
> after a short movment (probably the minimization see #1) the motion of the
> whole system stops for a while. Then it continues with movements at the
> point where constrains are decreased (probably, #2).
> I think, that the whole loop with the reassignTemp $TEMP is not working
> instead the whole system stays at 0.0 kelvin for this loop. I got that
> script from another person who is more skilled than me but not available
> right now. Anyway I am asking myself what the benefit of this whole loop was
> intended to be andI hasitate to change something right on my own without
> feedback.
> Hope you might help me. Have great day and Thank you!
> Best wishes,
> Daniel

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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