[gmx-users] Stimulation stopped at 2ns

[Justin Lemkul]

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.

> 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>
>>> 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> | (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 | (410) 706-7441

==================================================