AMBER Archive (2008)

Subject: Re: AMBER: problems with Replica Exchange

From: Carlos Simmerling (
Date: Thu Feb 28 2008 - 06:46:57 CST

the thing to try first is 1 processor per group. this way you
know that output from shake errors etc will get written to the
output file, which only the master process for each replica can do.
this is the same situation in normal MD- if there is a problem with no
error msg in the output always try to run single processor to test it.
you should not need anything special in the restart file from sander,
it can be used directly for remd. it's hard to help more since you haven't
told us much of anything about how you are doing the calculation.

are you using only 2 replicas?

does the same multisander job work fine if you just turn remd off (but
otherwise use exactly the same input files)?

On Thu, Feb 28, 2008 at 7:29 AM, <> wrote:
> Hello,
> I am trying to do Replica Exchange calculations using Amber 9. When I try with
> the files of the example of the tests, it works, but when I try with my protein
> I have problems. Using directly the usual restart file from a sander calculation
> I get problems of the type
> [1] MPI Abort by user Aborting program !
> [1] Aborting program!
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> srun: error: s30c1b04: task[0-1]: Exited with exit code 255
> However, when I create the restart file from the trajectory file with ptraj the
> calculation stops with no errors, but stop writting at the point (in the
> rem.out files):
> ...................
> trajectory generated by ptraj
> begin time read from input coords = 0.000 ps
> Number of triangulated 3-point waters found: 0
> | Atom division among processors:
> | 0 2573
> | Running AMBER/MPI version on 1 nodes
> | MULTISANDER: 2 groups. 1 processors out of 2 total.
> ....................
> It creates the correspondent files reminfo and rem.log, but they are all empty.
> In the error file I only can see "srun: Force Terminated job".
> Since the same calculation works with the protein that appears in the test
> examples, maybe could it be a problem of format? Should I do any special
> treatment to the restart file I use for the calculations?
> Thank you very much for you help, in advance.
> Rebeca García Fandiño Ph. D.
> Parc Cientific de Barcelona
> Barcelona Spain
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