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
> >
> _______________________________________________
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> 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
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Received on Fri Oct 25 2019 - 21:00:02 PDT
