[gmx-users] Stimulation stopped at 2ns

[Rama Krishna Koppisetti]

Thanks Justin for your reply,

I found something like this, in .log file,nsteps=1000000 but in .mdp file
it is nsteps=5000000. I don't see any stdout and stderr files.

_______________________________________________________
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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