[gmx-users] Replica Exchange MD
Mark Abraham
mark.j.abraham at gmail.com
Wed Oct 5 14:31:28 CEST 2016
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
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> > >
> > > --
> > > Thanks with regards
> > > Kalyanashis Jana
> > > --
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>
>
> --
> Thanks with regards
> Kalyanashis Jana
> --
> Gromacs Users mailing list
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