[gmx-users] Re:Simulation Crash

[Kishore]

Dear Justin,
I have used the same .mdp file you have used in your tutorial for
enzyme-ligand complex, I am pasting it here. My system consists of 10212
(enzyme+NADPH) atoms and 45000 water molecules.

title       = Protein-ligand complex NPT equilibration
define      = -DPOSRES  ; position restrain the protein and ligand
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 50000     ; 2 * 50000 = 100 ps
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 100       ; save coordinates every 0.2 ps
nstvout     = 100       ; save velocities every 0.2 ps
nstenergy   = 100       ; save energies every 0.2 ps
nstlog      = 100       ; update log file every 0.2 ps
energygrps  = Protein NDPH
; Bond parameters
continuation    = yes           ; first dynamics run
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 cells
nstlist     = 5         ; 10 fs
rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
rvdw        = 1.4       ; 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      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein_NDPH SOL_NA+    ; two coupling groups - more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 300   300                     ; reference temperature, one for
each group, in K
; Pressure coupling is off
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
NPT
pcoupltype  = isotropic                     ; uniform scaling of box vectors
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
compressibility = 4.5e-5                    ; isothermal compressibility of
water, 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       ; assign velocities from Maxwell distribution

-- 
KRISHNA KISHORE at IIT-MADRAS
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