[gmx-users] Replica Exchange MD
Kalyanashis Jana
kalyan.chem.in at gmail.com
Wed Oct 5 14:16:49 CEST 2016
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.
/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>]" 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
> > --
> > Gromacs Users mailing list
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--
Thanks with regards
Kalyanashis Jana
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