[gmx-users] distance restrained D simulations

Mark Abraham mark.abraham at anu.edu.au
Thu Sep 30 12:55:28 CEST 2010

----- Original Message -----
From: jayant james <jayant.james at gmail.com>
Date: Thursday, September 30, 2010 9:36
Subject: [gmx-users] distance restrained D simulations
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> > Hi!
> I am trying to perform distance restrained MD simulations of a protein with Gromacs4.0.5.
> I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am incorporating simular to NOE distance restraints in NMR.

The details of how you tried to do this are important. See http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm and consider section 5.4 of the manual. There might be a solution that does not have this issue.


>  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
> Thanks
> JJ
> 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 decomposition > 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
 > www.chick.com/reading/tracts/0096/0096_01.asp) 
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