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 <jalem...@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
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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@outerbanks.umaryland.**edu <jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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