Re: amber-developers: multiple targeted MD in amber11

From: Scott Brozell <>
Date: Wed, 30 Jul 2008 18:34:03 -0700 (PDT)


The mtmd test for sander.MPI fails if the number of processors is
greater than 1. The ./Run.mtmdtest check is
$numprocs > 2
Is the test check incorrect ?

% /tmp/amber11/test/mtmdtest ./Run.mtmdtest
SANDER: Multiply-targeted MD, new to AMBER 11
        Tested on an RNA duplex.
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.

PID 21314 failed on node n0 ( due to signal 11.
  ./Run.mtmdtest: Program error


On Thu, 3 Jul 2008, Volodymyr Babin wrote:

> thank you. I believe that the ncsu_pmd subsystem already implements
> this functionality (as a particular case when all collective variables
> are of MULTI_RMSD type with just one "group" each). In addition, the
> ncsu_pmd also modifies REMD exchange probabilities so that it should
> be possible to do umbrella sampling using parallel tempering.

On Thu, 3 Jul 2008, David Mathews wrote:

> Matt Seetin, from my group, has added a new feature to amber11 that allows
> for targeted MD to multiple targets (with multiple force constants,
> etc). We are using this for umbrella sampling. I've committed the changes
> to amber11 and, now that the amber tools are settling down for a release,
> we would appreciate any feedback. Of course, we want to know if we have
> broken anything (we are restricted to testing with various flavors of EM64
> linux using ifort, g95, and gfortran), but we also want to know whether
> this has enough broad appeal to keep in amber11. There is a new entry in
> the manual and a test case. We call this multiply-targeted MD (mtmd).
Received on Sun Aug 03 2008 - 06:07:19 PDT
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