[gmx-users] Stimulation stopped at 2ns
Nuno Azoia
nazoia at gmail.com
Mon Jul 8 23:20:59 CEST 2013
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.
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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