perhaps... there is no way to answer yes/no. REMD in explicit water can be
very computationally expensive, and challenging to do well especially on
your system that seems to be quite large. Having basic experience with REMD
might help. We can't really help more since we don't know anything about
your project or what you are trying to do.
If you want to use GB for REMD, I would suggest doing GB MD on your system
first to see how it behaves, and then to proceed to REMD only if the
simulations seem reasonable but MD does not provide enough sampling.
On Sun, Oct 27, 2019 at 11:44 PM Rinsha Chk <rinshachk.gmail.com> wrote:
> Since I didn't use GB in the previous MD run, can I use the same
> condition in remd?
>
> 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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> > > > >
> > > > >
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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 Mon Oct 28 2019 - 07:30:03 PDT
