it might... you might try some gentle heating first. REMD in explicit water
is going to be challenging, and may not really give better results than
some heating/cooling cycles (it should in principle, but in practice on a
large system may not really be thermodynamically converged)
On Mon, Oct 28, 2019 at 11:59 PM Rinsha Chk <rinshachk.gmail.com> wrote:
> Thank you very much, Carlos, for your suggestions and time...
> I am doing REMD for sampling the conformational space sufficiently, to
> check whether my ligand is stuck in any local minima during MD. Since REMD
> is capable of overcoming high-energy barriers easily and sampling
> conformational space sufficiently, I thought REMD might help.
>
> On Mon, Oct 28, 2019 at 7:53 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 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.
> > > > > > > > > _______________________________________________
> > > > > > > > > AMBER mailing list
> > > > > > > > > AMBER.ambermd.org
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> > > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
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> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
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> > > >
> > >
> > >
> > > --
> > > Rinsha. C H
> > > Research Scholar
> > > Theoretical and Computational Chemistry Lab
> > > Department of Chemistry
> > > NIT Calicut
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
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> > >
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> > 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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Received on Tue Oct 29 2019 - 11:00:03 PDT
