On Tue, 2014-05-20 at 18:56 +0530, Sanjib Paul wrote:
> *Warning: Conflicting CPU frequencies detected, using: 2600.000000.Warning:
> Conflicting CPU frequencies detected, using: 2600.000000.*
> In NPT it stopped after giving some message -
This looks like a problem that could be related to your MPI. I don't
know how to solve this warning, and seems unrelated to Amber. I suggest
trying to google the warning message.
>
> *MPI_ABORT was invoked on rank 1 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
> onexactly when Open MPI kills
> them.--------------------------------------------------------------------------|
> ERROR: PMEMD does not support intermolecular
This often indicates that your topology file is broken. You can use
ParmEd to check your topology file, and if problems are detected it will
try to suggest ways to fix it. For instance:
parmed.py -p prmtop
then at the prompt, type the command:
checkValidity
hopefully this gives you helpful information.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 20 2014 - 07:00:04 PDT
