On 12/01/2012 5:29 PM, bharat gupta wrote:
Thanks for the advice I re-complied everything again with static
libraries and the installation went fine. But while executing the
following command I am again getting error :-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 500 -v
Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (3)
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
Halting program mdrun_mpi
gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
I am trying to simulate 5 replicas and I have 4 cpu .
See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps
point 2. You cannot simulate an arbitrary number of replicas on an
arbitrary number of processors.
Mark
On Thu, Jan 12, 2012 at 1:37 PM, lina <lina.lastn...@gmail.com
<mailto:lina.lastn...@gmail.com>> wrote:
On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:
Hi,
I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am
getting the
following error:-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries:
libgmx_mpi.so.6: cannot
enable executable stack as shared object requires: Permission
denied
Can you run a normal md smoothly?
try:
mdrun_mpi mdrun -deffnm prefix_0
if it works, then some of your trajectories not sound. means
system does not equilibrium well.
Can anybody suggest me how could I rectify this error.
--
Bharat
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
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