AMBER Archive (2008)

Subject: AMBER: writing out a distance between two atoms in sander

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Mon Mar 10 2008 - 08:33:55 CDT

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
Vlad 

-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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