Running REMD

From: Nicolas Martin (nicolasmartin973_at_gmail.com)
Date: Wed Sep 14 2016 - 03:10:55 CDT

Dear users,

I am trying to run bias exchange umbrella sampling and read in this
tutorial
(http://www.ks.uiuc.edu/Training/Tutorials/science/umbrella/REUS-1D.pdf)
that there is no official NAMD command or colvar module for doing so. I
figure out I might as well start with running temperature exchange and
then change the script to perform bias exchange (BEUS) and not
temperature exchange but to avoid non productive use of my time I wanted
to know if any of you had a TCL script to do so or a in house tutorial
that I could follow.

Running the tutorial mentioned above I'm getting an error as shown
bellow. Sorry for the super long text but I don't know what is relevant
to shown you. I'm running on a 32 cores machine. Does any of you know
what I am doing wrong ?

XXXXX_at_nXXX:~/umbrella_1d$ mpirun -np 16
NAMD_2.10_Linux-x86_64-netlrts/namd2 +replicas 16 job0.conf +stdout
output/%d/job0.%d.log
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 30840 on node n304 exited on
signal 6 (Aborted).
--------------------------------------------------------------------------
10 total processes killed (some possibly by mpirun during cleanup)
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
Charm++: standalone mode (not using charmrun)
Charm++> Running in non-SMP mode: numPes 1
namd2: machine-common-core.c:863: create_partition_map: Assertion
`(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.

I finally, I have a more general question to the NAMD community. Why is
replica exchange not implemented in NAMD and one has to use this TCL
script ? Isn't it decreasing the performances ? From what I have seen it
is implement in PLUMED and other codes such as GROMACS.

Cheers, and thank you in advance for you help and advices,

NM

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