AMBER: print distance between atoms during simulation within sander itsself

From: Vlad Cojocaru <>
Date: Fri, 15 Feb 2008 15:06:24 +0100

Dear amber users,

Is there a way to print the distance between two groups of atoms during
the simulation within sander itsself ? I am asking becuase I would like
to print a distance more often than the interval between two trajectory
frames .

I was thinking of using a "pseudo" restraint with rk1-rk4 force
constants equal to 0, in combination with a " &wt type='DUMPFREQ',
istep1=5, / " card but the problem is that I want to do that in
combination with jar=1 (steered MD) and jar=1 accepts only a single
restraint defined in the DISANG file.

Any thoughts of how one can do that ?

Best wishes

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
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Received on Sun Feb 17 2008 - 06:07:36 PST
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