AMBER Archive (2008)

Subject: AMBER: 100 short MD runs within a single Sander script?

From: Sebastian Stolzenberg (
Date: Fri Jun 06 2008 - 23:55:37 CDT

Hi everybody,

(how) is it possible to write a single Sander script doing the following:

1.) Given a trajectory file (with say 100 frames), the Sander script
takes each of these 100 frames as initial structures for short MD
runs, say 40fs.
2.) It determines some order parameter (e.g. a torsion angle), maybe
also determines an average, and outputs the data into a seperate
external file.

I am mostly interested in point 1.)
All this works with CHARMM, but I know that for my systems, single
Amber MD runs are much faster than CHARMM ones.

Thank you very much for your help,
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