[AMBER] About difference between Sander and Pmemd

From: Bin Wu <wubin2002.gmail.com>
Date: Wed, 15 Jun 2011 22:54:38 -0400

Dear Amber Users

Thank you so much for your previous help. Now I turn to Pmemd for parallel
computation. However, I am a little bit confused by the simulation results.

Using pmemd, the trajectory of particles visualized from VMD seems odd. A
couple of chemical bonds seem to break or two bonded atoms come abnormally
far separated. In contrary to the simulation result from Pmemd, the
trajectory obtained using Sander seems pretty normal. No bond breaking is
observed. (The syntax and input, prmtop as well as inpcrd files are
identical for two cases, which are attached to this email.)

Therefore, I wonder simulation results from Pmemd and Sander are supposed to
be different or I compiled Pmemd wrong, because the process of Pmemd
installation is not smooth at all. And I got several passes and an error in
the end when I do "make test.pmemd". The error message is printed below.

export TESTsander='../../../../exe/pmemd'; cd chamber/md_engine/dhfr &&
/bin/sh: ./Run.dhfr_charmm.min: Permission denied
make: *** [test.pmemd] Error 126

I would be grateful if someone could give me some hint or direction.

Thank you very much.

Best Regards!


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Received on Wed Jun 15 2011 - 20:00:04 PDT
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