AMBER Archive (2008)

Subject: AMBER: problems with Replica Exchange

From: rebeca_at_mmb.pcb.ub.es
Date: Thu Feb 28 2008 - 06:29:23 CST

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
rebeca_at_mmb.pcb.ub.es

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