[gmx-users] Stimulation stopped at 2ns
Florian Dommert
dommert at icp.uni-stuttgart.de
Tue Jul 9 10:02:59 CEST 2013
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Nuno Azoia
> Sent: Monday, July 08, 2013 11:21 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Stimulation stopped at 2ns
>
> On 8 July 2013 22:12, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 7/8/13 5:08 PM, Rama Krishna Koppisetti wrote:
> >
> >> Thanks Justin for your reply,
> >>
> >> I found something like this, in .log file,nsteps=1000000 but in .mdp
file
> >>
> >
> > Then you're not using the .mdp file you think you are and the run is
only
> > scheduled for 2 ns.
>
>
> After changing the .mdp file, did you run grompp again? And did you get a
> new .tpr file? I already had a similar problem. Sometimes; and I not sure
> about the gromacs version on that time, I just run grompp with new
> parameters in the .mdp file but grompp did not change the .tpr file, if
> already present.
>
Did you already ran gmxdump on the tpr file you used? Then you will
immediately see, how many steps are set in the tpr file.
/Flo
>
> Cheers
> Nuno Azoia
>
> >
> >
> > it is nsteps=5000000. I don't see any stdout and stderr files.
> >>
> >>
> > These are standard streams, not files. Some queuing systems and other
> > software save their output, others don't.
> >
> > -Justin
> >
> >
> > ______________________________**_________________________
> >> On Mon, Jul 8, 2013 at 3:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >>>
> >>> On 7/8/13 4:33 PM, Rama wrote:
> >>>
> >>> Dear All,
> >>>>
> >>>> I'm trying to do long stimulation run but every time it stops at 2ns,
> >>>> below
> >>>> pasted .mdp file parameters. How to run 10ns or more ns stimulation
run?
> >>>> Do
> >>>> I need to change any parameters in .mdp file or else where.
> >>>>
> >>>>
> >>>> There is nothing in the .mdp file that would cause the run to stop.
> >>> Either the simulation is crashing or you have some queuing system
that
> >>> is
> >>> terminating the job. Check stdout, stderr, and .log file(s) for
> >>> information.
> >>>
> >>> -Justin
> >>>
> >>>
> >>> Thanks in Advance.
> >>>
> >>>> -------------
> >>>>
> >>>> title = Protein-DMPC bilayer Production MD
> >>>> ; Run parameters
> >>>> integrator = md ; leap-frog integrator
> >>>> nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns)
> >>>> dt = 0.002 ; 2 fs
> >>>> ; Output control
> >>>> nstxout = 100000 ; save coordinates every 200
ps
> >>>> nstvout = 100000 ; save velocities every 200
ps
> >>>> nstxtcout = 50000 ; xtc compressed trajectory output
every
> >>>> 100 ps
> >>>> nstenergy = 50000 ; save energies every 100 ps
> >>>> nstlog = 100000 ; update log file every 200
ps
> >>>> ; Bond parameters
> >>>> continuation = yes ; Restarting after NPT
> >>>> constraint_algorithm = lincs ; holonomic constraints
> >>>> constraints = all-bonds ; all bonds (even heavy
atom-H
> >>>> bonds)
> >>>> constrained
> >>>> lincs_iter = 1 ; accuracy of LINCS
> >>>> lincs_order = 4 ; also related to
accuracy
> >>>> ; Neighborsearching
> >>>> ns_type = grid ; search neighboring grid cels
> >>>> nstlist = 5 ; 10 fs
> >>>> rlist = 1.2 ; short-range neighborlist cutoff (in
> >>>> nm)
> >>>> rcoulomb = 1.2 ; short-range electrostatic cutoff
(in
> >>>> nm)
> >>>> rvdw = 1.2 ; short-range van der Waals cutoff
(in
> >>>> nm)
> >>>> ; Electrostatics
> >>>> coulombtype = PME ; Particle Mesh Ewald for long-range
> >>>> electrostatics
> >>>> pme_order = 4 ; cubic interpolation
> >>>> fourierspacing = 0.16 ; grid spacing for FFT
> >>>> ; Temperature coupling is on
> >>>> tcoupl = Nose-Hoover ; More accurate
thermostat
> >>>> tc-grps = CA_ZN_DMPC_Protein SOL_CL ; three coupling
groups
> >>>> -
> >>>> more accurate
> >>>> tau_t = 0.5 0.5
> >>>> ; time
> >>>> constant, in ps
> >>>> ref_t = 310 310
> >>>> ; reference
> >>>> temperature, one for each group, in K
> >>>> ; Pressure coupling is on
> >>>> pcoupl = Parrinello-Rahman ; Pressure coupling on in
> >>>> NPT
> >>>> pcoupltype = semiisotropic ; uniform scaling of x-y
box
> >>>> vectors,
> >>>> independent z
> >>>> tau_p = 2.0 ; time constant, in
ps
> >>>> ref_p = 1.0 1.0 ; reference pressure,
> >>>> x-y, z (in bar)
> >>>> compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility,
> >>>> bar^-1
> >>>> ; Periodic boundary conditions
> >>>> pbc = xyz ; 3-D PBC
> >>>> ; Dispersion correction
> >>>> DispCorr = EnerPres ; account for cut-off vdW scheme
> >>>> ; Velocity generation
> >>>> gen_vel = no ; Velocity generation is off
> >>>> ; COM motion removal
> >>>> ; These options remove motion of the protein/bilayer relative to the
> >>>> solvent/ions
> >>>> nstcomm = 1
> >>>> comm-mode = Linear
> >>>> comm-grps = Protein_DMPC SOL_CL
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> View this message in context: http://gromacs.5086.x6.nabble.****
> >>>> com/Stimulation-stopped-at-****2ns-tp5009669.html<http://**
> >>>> gromacs.5086.x6.nabble.com/**Stimulation-stopped-at-2ns-**
> >>>> tp5009669.html<http://gromacs.5086.x6.nabble.com/Stimulation-
> stopped-at-2ns-tp5009669.html>
> >>>> >
> >>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> >>>>
> >>>>
> >>>> --
> >>> ==============================****====================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Postdoctoral Associate
> >>>
> >>> Department of Pharmaceutical Sciences
> >>> School of Pharmacy
> >>> Health Sciences Facility II, Room 601
> >>> University of Maryland, Baltimore
> >>> 20 Penn St.
> >>> Baltimore, MD 21201
> >>>
> >>> jalemkul at outerbanks.umaryland.****edu <jalemkul at outerbanks.**
> >>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>> | (410)
> >>> 706-7441
> >>>
> >>> ==============================****====================
> >>>
> >>> --
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> > --
> > ==============================**====================
> >
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Associate
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.**edu
> <jalemkul at outerbanks.umaryland.edu> | (410)
> > 706-7441
> >
> > ==============================**====================
> >
> > --
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> Nuno Gonçalo Azoia Lopes
>
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> 4705-473 Escudeiros
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