okay...
On Sat, Oct 26, 2019 at 5:04 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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> > > > > > AMBER.ambermd.org
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> > > >
> > > >
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--
Rinsha. C H
Research Scholar
Theoretical and Computational Chemistry Lab
Department of Chemistry
NIT Calicut
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Received on Sun Oct 27 2019 - 21:00:02 PDT
