milad ekramnia wrote:
Dear gromacs users
I am working with gromacs 4.0 and my system is a protein under tension solvated in water under Lincs constraint .when I run my mdrun over n nodes by mpirun I'll get n-1 trajectory files (also the same happen for all other output files ) which as it appears all are identical.
as far as I know each file shall represent a separate part of the box but when I analyze the trrs the results are identical ( e.g for g_gyrate task )
I want to now if they are exactly the same ? if yes , can I prevent the rest of them from being biult up ?
my mdrun command line is : mpirun -n 4 mdrun_mpi -v -s topol.tpr
Is -n the appropriate option? Some MPI implementations are different (-np, -N,
etc), and/or you may need to supply a hostfile.
and the grommp command is: grompp_mpi -v -c minimized.gro -p topol.top -f pull.mdp -n index.ndx
I also added --enabled-mpi to my mdrun command line but it didn't work .
If you did "--enabled-mpi" then that is incorrect, and you probably didn't
actually compile with MPI support. The proper configuration option is
"--enable-mpi" so you should check that you did not make a typo when installing
Gromacs.
-Justin
thanks
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
