[gmx-users] distance restrained D simulations

[Justin A. Lemkul]

jayant james wrote:
> 
> 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.
> 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

As the note tells you, use particle decomposition.  Long distance restraints 
can't be split over domain decomposition cells.

-Justin

> 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 
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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