AMBER: writing out a distance between two atoms in sander

From: Vlad Cojocaru <>
Date: Mon, 10 Mar 2008 14:33:55 +0100

Dear Amber users,

Is there a simple way to make sander output the distnce between two
atoms during the MD run without using restraints defined with force
constants equal to 0?

I am asking because I would like to write out a non-restrained distance
much more often than the trajectory frame output. I thought of using the
restraints capabilities of sander to defined a pseudo-restraint in which
the force constants are all equal to 0 but I am running an SMD
simulation in which a different distance is subject to the
time-dependent restraint and this type of simulaton only allows 1
restraint to be defined in the RST file.

Thanks for any tips

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 Wed Mar 12 2008 - 06:07:21 PDT
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