That's what I meant by the equilibration - is this input the same as your
prior md production run?
The problem with not finding the mein files is likely in the job scripts,
which you haven't shown us. You either have a typo, or aren't in the right
directory, or something like that. You could add something to the script to
check these things.
On Fri, Oct 25, 2019, 11:36 PM Rinsha Chk <rinshachk.gmail.com> wrote:
> okay... I got it...and modified remd.in as follows.
>
> remd
> &cntrl
> irest=0, ntx=1,
> nstlim=500, dt=0.002,
> irest=0, ntt=3, gamma_ln=1.0,
> temp0=XXXXX, ig=RANDOM_NUMBER,
> ntc=2, ntf=2, nscm=1000,
> ntb=0, 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
>
> But still, the same error appears.
> I didn't perform minimization and equilibrations, since, the starting
> geometry is taken from the classical MD production simulation trajectories
> that I already have, and trying to perform remd directly on this geometry.
> Is that will cause any issue?
>
> On Sat, Oct 26, 2019 at 1:04 AM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 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.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Rinsha. C H
> Research Scholar
> Theoretical and Computational Chemistry Lab
> Department of Chemistry
> NIT Calicut
> _______________________________________________
> AMBER mailing list
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>
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Received on Sat Oct 26 2019 - 03:30:02 PDT
