I can't suggest much for the filename issue, since it's either your file
system or perhaps your script doesn't put you in the right directory. This
should not be an Amber problem.
However I wonder about your mdin file - is this like what you used for the
equilibration MD? I'm not sure that it makes sense to use igb=5 and
ntb=2... I don't think that should even run.
On Fri, Oct 25, 2019 at 12:25 AM Rinsha Chk <rinshachk.gmail.com> wrote:
> Dear AMBER users,
> I am trying to perform Replica Exchange MD (REMD) simulation, with 8
> replicas and the input file used to generate the eight remd-input files is
> given below:
>
> remd
> &cntrl
> irest=0, ntx=1,
> nstlim=500, dt=0.002,
> irest=0, ntt=1, tautp=0.1,
> temp0=XXXXX, ig=RANDOM_NUMBER,
> ntc=2, ntf=2, nscm=1000,
> ntb=2, igb=5,
> cut=999.0, rgbmax=999.0,
> ntr=1,restraint_wt=0.5,restraintmask='(:1-412 & .CA)',
> ntpr=100, ntwx=1000, ntwr=100000,
> nmropt=1,
> numexchg=1000,
> /
> &wt TYPE='END'
> /
> DISANG=tea-c_chir.dat
>
> I didn't perform minimization and equilibrations, since, the starting
> geometry is taken from the classical MD production simulation trajectories
> that I already have.
>
> when i used the command,
>
> "/export/apps/intel19/compilers_and_libraries_2019.3.199/linux/mpi/intel64/bin/mpirun
> -np 8 -hostfile $PBS_NODEFILE
> /export/apps/Amber18/amber18/bin/pmemd.cuda.MPI -ng 8 -groupfile
> remd.groupfile"
> to run the simulation, i encountered with the following error:
>
>
> Unit 5 Error on OPEN: remd-004.in
>
>
>
>
> Unit 5 Error on OPEN: remd-002.in
>
>
>
> Abort(1) on node 1 (rank 1 in comm 0): application called
> MPI_Abort(MPI_COMM_WORLD, 1) - process 1
>
> When I tried the same with pmemd.MPI the error is "Abort(1) on node 1 (rank
> 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1"
>
> How can I solve this error? Am I supposed to modify my input files?
>
>
> Thanks in advance.
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>
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Received on Fri Oct 25 2019 - 13:00:01 PDT
