It's still a bit confusing - this seems to have been done in explicit
solvent, but in remd you are switching to gb? You might want to do the MD
in GB before removing the water and doing remd. It could be hard to
determine if problems are form remd or from removing the explicit water.
On Sat, Oct 26, 2019, 7:12 AM Rinsha Chk <rinshachk.gmail.com> wrote:
> The inputs are not the same. The "equilibration" input is given below:
> &cntrl
> imin=0,irest=1, ntx=5,
> dielc=1.0, cut=9.0,
> ntt=1, temp0=300.0, tautp=0.1,
> ntp=1, taup=0.1,
> ntb=2, ntc=2, ntf=2,iwrap=0,
> nstlim=5000000, dt=0.002,ntwx=5000,
> ntr=1,restraint_wt=0.5,restraintmask='(:1-412 & .CA)',
> ntpr=500, ntwr=500,
> &end
> and I'm trying to perform REMD on a particular structure resulted from this
> trajectory.
>
> On Sat, Oct 26, 2019 at 3:57 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 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.
> > > > > _______________________________________________
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> > >
> > >
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Received on Sat Oct 26 2019 - 05:00:01 PDT
