AMBER Archive (2008)

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

From: Vlad Cojocaru (
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

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 ----------------------------------------------------------------------------

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to