AMBER: print distance between atoms during simulation within sander itsself

From: Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de>
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 ?

Thanks
Best wishes
vlad 

-- 
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Dr. Vlad Cojocaru
EML Research gGmbH
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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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Received on Sun Feb 17 2008 - 06:07:36 PST
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