Re: [AMBER] About difference between Sander and Pmemd

From: Bin Wu <>
Date: Thu, 16 Jun 2011 21:24:54 -0400

Thank you very much for your reply.

I am pretty sure that my simulation results obtained from Sander and Pmemd
are different. The evident difference would be the bond breaking phenomena
in Pmemd which are absent in the case of Sander.

As for the previously mentioned "Permission denied" while I launched "make
test.pmemd", I figured out the problem was that the test script was not set
as executable. After I enabled them as executables, the test process went on
without any trouble. And I looked into the test cases showing "Possible
failure", there are only very subtle differences between the simulation
results got from my machine and the references, which make me believe they
are just rounding errors.

I am very confused. Since my installation could pass those test, does not
that mean I install pmemd correctly? And if that is true, why my simulation
results from Sander and Pmemd are so different?

I would be very grateful if someone can help me with this issue.

Thank you very much for your attention.

Best Regards!


2011/6/16 David A Case <>

> On Wed, Jun 15, 2011, Bin Wu wrote:
> >
> >
> > Therefore, I wonder simulation results from Pmemd and Sander are supposed
> to
> > be different
> Sander and pmemd should give identical results; indeed, the test cases for
> pmemd are the same as those for sander, just running a different
> executable.
> But be sure to read section 1.3.4 of the Users' Manual, which discusses
> numerical differences between programs.
> Check your visualization to be sure there is not some imaging problem. Of
> course, it is also possible that you have uncovered some bug. Check the
> coordinates of atoms that should be bonded to be sure they have indeed
> separated.
> > or I compiled Pmemd wrong, because the process of Pmemd
> > installation is not smooth at all.
> Details would help. Compiling pmemd is supposed to be completely smooth
> (always is for me). But there are an enormous number of combinations of
> compilers and operating systems, so we need to know details of what went
> wrong.
> >
> > export TESTsander='../../../../exe/pmemd'; cd chamber/md_engine/dhfr &&
> > ./Run.dhfr_charmm.min
> > /bin/sh: ./Run.dhfr_charmm.min: Permission denied
> > make: *** [test.pmemd] Error 126
> This is odd, and I do not recall seeing such a message before. Check the
> permissions on the file involved: is it indeed executable? What happens if
> you try to execute that script by hand?
> ....dac
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Received on Thu Jun 16 2011 - 18:30:03 PDT
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