for (1), can you be more specific about what information you are seeking?
Amber 22 can save files in ascii format, but netcdf is usually preferable
and is fully compatible with REMD.
for (2), yes pmemd.cuda.MPI works with REMD and the command that you used
is comparable to ones that work for me in REMD. Have other MPI jobs worked
for you?
On Wed, Nov 9, 2022 at 8:43 AM Munazzah Fatima Ansari via AMBER <
amber.ambermd.org> wrote:
> 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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>
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Received on Thu Nov 17 2022 - 09:00:03 PST
