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.abra...@gmail.com> wrote: > Hi, > > On Wed, Oct 5, 2016 at 2:17 PM Kalyanashis Jana <kalyan.chem...@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.abra...@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...@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.papada...@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-boun...@maillist.sys.kth.se < > > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > > > > > Kalyanashis Jana <kalyan.chem...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.