Hi,
1. I was performing replica exchange method from Amber tutorial. In the
tutorial developers use Amber16, and they get the remd.mdcrd* files in
human-readable format which contain the information of the replica
number, exchange number, MD step number, and thermostat temperature. I
am using Amber22, remd.mdcrd* files are in binary format. I use cpptraj
to generate the trajectory file, but it doesn't contain the replica
exchange information. From which file do I get the information of
replica exchange at different temperatures?
2. I also use pmemd.cuda.MPI for replica exchange method with command "
mpirun -np 8 pmemd.cuda.MPI -ng 8 -groupfile remd.groupfile"
and I came up with the error:
setup_groups: MPI size is not a multiple of -ng
--------------------------------------------------------------------------
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.
Is the pmemd.cuda.MPI is available for REMD simulation. If yes, Is there
is some tutorial available for it, or what are the basic flags or
commands?
Regards,
Munazzah Fatima Ansari
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Received on Wed Nov 09 2022 - 06:00:02 PST
