[gmx-users] distance restrained D simulations

jayant james jayant.james at gmail.com
Thu Sep 30 01:35:40 CEST 2010

I am trying to perform distance restrained MD simulations of a protein with
I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am
incorporating simular to NOE distance restraints in NMR.
When I use one processor for the simulations its all fine, but, when I use
multiple processors I get a bunch of errors
lets me start with the "NOTE" found below. Well do not want to increase the
cut-off distance but want the program to use multiple processors. How can I
overcome this problem?
I would appreciate your input

NOTE: atoms involved in distance restraints should be within the longest
cut-off distance, if this is not the case mdrun generates a fatal error, in
that case use particle decomposition (mdrun option -pd)

WARNING: Can not write distance restraint data to energy file with domain
Loaded with Money

Program mdrun_mpi, VERSION 4.0.5
Source code file: ../../../src/mdlib/domdec.c, line: 5873

Fatal error:
There is no domain decomposition for 4 nodes that is compatible with the
given box and a minimum cell size of 8.89355 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

"What Kind Of Guru are You, Anyway ?" (F. Zappa)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 4

gcq#21: "What Kind Of Guru are You, Anyway ?" (F. Zappa)

mpirun has exited due to process rank 2 with PID 28700 on
node compute-3-73.local exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

Jayasundar Jayant James

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