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