[gmx-users] Replica Exchange MD
Kalyanashis Jana
kalyan.chem.in at gmail.com
Thu Oct 6 10:30:45 CEST 2016
Thank you very much for your reply and suggestions. I am discussing with
system admin regarding this issue.
With Best Regards,
Kalyanashis Jana
On Wed, Oct 5, 2016 at 6:01 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> On Wed, Oct 5, 2016 at 2:17 PM Kalyanashis Jana <kalyan.chem.in at gmail.com>
> wrote:
>
> > Hi Mark,
> > The MD run stopped after 52.9 ps and the error is
> > "MPI: STDOUT or STDERR buffer exhausted.
> > MPI: Set MPI_UNBUFFERED_STDIO or output no more than about 8192
> characters
> > MPI: between newlines
>
>
> Your MPI library makes assumptions about the MPI application that are
> inappropriate. mdrun expects to be able to write to stdout and it works
> like stdout.
>
> Either set the MPI_UNBUFFERED_STDIO variable like it suggests (please talk
> to your sysadmins and/or documentation for how to do this, I have no idea,
> and little interest in SGI's MPI implementation that causes me as many
> problems as all the other implementations put together :-)), or use any
> other MPI library you have available.
>
> Mark
>
>
> > /opt/sgi/mpt/mpt-2.01/bin/mpiexec_mpt: line 52: 29708 Killed
> > $mpicmdline_prefix -f $paramfile"
> >
> >
> > I have pasted the equil.mdp, more less similar to the REMD tutorial, for
> > your kind perusal.
> >
> >
> > include =
> > define =
> > integrator = md
> > tinit = 0
> > dt = 0.001
> > nsteps = 500000
> > init-step = 0
> > simulation-part = 1
> > comm-mode = Linear
> > nstcomm = 100
> > comm-grps =
> > bd-fric = 0
> > ld-seed = 1993
> > emtol = 10
> > emstep = 0.01
> > niter = 20
> > fcstep = 0
> > nstcgsteep = 1000
> > nbfgscorr = 10
> > rtpi = 0.05
> > nstxout = 250
> > nstvout = 1000
> > nstfout = 0
> > nstlog = 100
> > nstcalcenergy = 100
> > nstenergy = 1000
> > nstxtcout = 0
> > xtc-precision = 1000
> > xtc-grps =
> > energygrps =
> > ;cutoff-scheme = Verlet
> > nstlist = 10
> > ns-type = Grid
> > pbc = xyz
> > periodic-molecules = no
> > ;verlet-buffer-drift = 0.005
> > rlist = 1
> > rlistlong = -1
> > ;nstcalclr = -1
> > coulombtype = PME
> > ;coulomb-modifier = Potential-shift-Verlet
> > rcoulomb-switch = 0
> > rcoulomb = 1
> > epsilon-r = 1
> > epsilon-rf = 0
> > vdw-type = Cut-off
> > ;vdw-modifier = Potential-shift-Verlet
> > rvdw-switch = 0
> > rvdw = 1
> > DispCorr = No
> > table-extension = 1
> > energygrp-table =
> > fourierspacing = 0.12
> > fourier-nx = 0
> > fourier-ny = 0
> > fourier-nz = 0
> > pme-order = 6
> > ewald-rtol = 1e-05
> > ewald-geometry = 3d
> > epsilon-surface = 0
> > optimize-fft = yes
> > implicit-solvent = No
> > gb-algorithm = Still
> > nstgbradii = 1
> > rgbradii = 1
> > gb-epsilon-solvent = 80
> > gb-saltconc = 0
> > gb-obc-alpha = 1
> > gb-obc-beta = 0.8
> > gb-obc-gamma = 4.85
> > gb-dielectric-offset = 0.009
> > sa-algorithm = Ace-approximation
> > sa-surface-tension = -1
> > tcoupl = v-rescale
> > nsttcouple = -1
> > nh-chain-length = 10
> > ;print-nose-hoover-chain-variables = no
> > tc-grps = system
> > tau-t = 0.1
> > ref-t = 280.00
> > pcoupl = No
> > pcoupltype = Isotropic
> > nstpcouple = -1
> > tau-p = 1
> > compressibility =
> > ref-p =
> > refcoord-scaling = No
> >
> > QMMM = no
> > QMMM-grps =
> > QMmethod =
> > QMMMscheme = normal
> > QMbasis =
> > QMcharge =
> > QMmult =
> > SH =
> > CASorbitals =
> > CASelectrons =
> > SAon =
> > SAoff =
> > SAsteps =
> > MMChargeScaleFactor = 1
> > bOPT =
> > bTS =
> > annealing =
> > annealing-npoints =
> > annealing-time =
> > annealing-temp =
> > gen-vel = yes
> > gen-temp = 280.00
> > gen-seed = 173529
> > constraints = all-bonds
> > constraint-algorithm = Lincs
> > continuation = no
> > Shake-SOR = no
> > shake-tol = 0.0001
> > lincs-order = 4
> > lincs-iter = 1
> > lincs-warnangle = 30
> > morse = no
> > energygrp-excl =
> > nwall = 0
> > wall-type = 9-3
> > wall-r-linpot = -1
> > wall-atomtype =
> > wall-density =
> > wall-ewald-zfac = 3
> > pull = no
> > ;rotation = no
> > disre = No
> > disre-weighting = Conservative
> > disre-mixed = no
> > disre-fc = 1000
> > disre-tau = 0
> > nstdisreout = 100
> > orire = no
> > orire-fc = 0
> > orire-tau = 0
> > orire-fitgrp =
> > nstorireout = 100
> > free-energy = no
> > couple-moltype =
> > couple-lambda0 = vdw-q
> > couple-lambda1 = vdw-q
> > couple-intramol = no
> > init-lambda = -1
> > ;init-lambda-state = -1
> > delta-lambda = 0
> > nstdhdl = 50
> > fep-lambdas =
> > mass-lambdas =
> > coul-lambdas =
> > vdw-lambdas =
> > bonded-lambdas =
> > restraint-lambdas =
> > temperature-lambdas =
> > ;calc-lambda-neighbors = 1
> > init-lambda-weights =
> > ;dhdl-print-energy = no
> > sc-alpha = 0
> > sc-power = 1
> > ;sc-r-power = 6
> > sc-sigma = 0.3
> > ;sc-coul = no
> > separate-dhdl-file = yes
> > dhdl-derivatives = yes
> > dh_hist_size = 0
> > dh_hist_spacing = 0.1
> > acc-grps =
> > accelerate =
> > freezegrps =
> > freezedim =
> > cos-acceleration = 0
> > deform =
> > ;simulated-tempering = no
> > ;simulated-tempering-scaling = geometric
> > ;sim-temp-low = 300
> > ;sim-temp-high = 300
> > E-x =
> > E-xt =
> > E-y =
> > E-yt =
> > E-z =
> > E-zt =
> > ;adress = no
> > user1-grps =
> > user2-grps =
> > userint1 = 0
> > userint2 = 0
> > userint3 = 0
> > userint4 = 0
> > userreal1 = 0
> > userreal2 = 0
> > userreal3 = 0
> > userreal4 = 0
> >
> > With Best Regards,
> > Kalyanashis Jana
> >
> > On Wed, Oct 5, 2016 at 4:18 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > "It has been abnormally terminated" is too vague to lead to effective
> > help.
> > > What did the terminal and log files say about what led to termination?
> > >
> > > Mark
> > >
> > > On Wed, Oct 5, 2016 at 12:43 PM Kalyanashis Jana <
> > kalyan.chem.in at gmail.com
> > > >
> > > wrote:
> > >
> > > > Dear Sotirios,
> > > > Thank you very much for your reply. I have used ΔΤ=10 K, 5K and
> 3K...
> > > But
> > > > it has been abnormally terminated.
> > > > Is there any possible solution? Please help me...
> > > > Thanks in advance,
> > > > Kalyanashis
> > > >
> > > > On Wed, Oct 5, 2016 at 12:02 PM, Sotirios Dionysios I. Papadatos <
> > > > si.papadatos at edu.cut.ac.cy> wrote:
> > > >
> > > > > In this case maybe, just maybe there is a big gap between
> > temperatures.
> > > > > Hence the ΔΕ is to large and the exchange destabilizes your system.
> > > Try a
> > > > > dummy run with a small ΔΤ to see if this is the case
> > > > >
> > > > > ________________________________
> > > > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > > > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> > > > > Kalyanashis Jana <kalyan.chem.in at gmail.com>
> > > > > Sent: Tuesday, October 4, 2016 9:40:08 PM
> > > > > To: Discussion list for GROMACS users
> > > > > Subject: [gmx-users] Replica Exchange MD
> > > > >
> > > > > Dear all,
> > > > > I am trying to perform a REMD simulation for a protein drug
> complex.
> > I
> > > > have
> > > > > followed REMD tutorial (
> > > > > http://www.gromacs.org/Documentation/Tutorials/
> > > GROMACS_USA_Workshop_and_
> > > > > Conference_2013/An_introduction_to_replica_
> > > exchange_simulations%3A_Mark_
> > > > > Abraham,_Session_1B
> > > > > ).
> > > > > I have prepared 10 set for the REMD simulation and generated the
> tpr
> > > file
> > > > > for MD run. I have used "mpirun -np 10 mdrun_mpi -v -multidir
> > > > > equil[0123456789 <0123-45%2067%2089> <0123-45%2067%2089>]" for MD
> > run. It has been
> > > > abnormally terminated at the
> > > > > middle of the MD run. However, the same topol.tpr files have
> > produced
> > > > > normally terminated MD run when the simulations have been run
> > > > > individually using
> > > > > "mpirun -np 10 mdrun_mpi -v -s topol.tpr ........"
> > > > > Please suggest me, how can I overcome this problem.
> > > > > Looking forward to hear from you.
> > > > >
> > > > >
> > > > > Thanks in advance,
> > > > > Kalyanashis Jana
> > > > >
> > > > >
> > > > > --
> > > > > Thanks with regards
> > > > > Kalyanashis Jana
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Thanks with regards
> > > > Kalyanashis Jana
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> >
> > --
> > Thanks with regards
> > Kalyanashis Jana
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
--
Thanks with regards
Kalyanashis Jana
More information about the gromacs.org_gmx-users
mailing list