[gmx-users] run.mdp on 4.6-gpu

[Steven Neumann]

Dear Gmx Users,

Could you please assess my mdp file on GPUs:

title       = Protein-ligand complex MD simualation
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 100000000    ; 200 ns
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 0     ; suppress .trr output ; output coordinates every 25 ps
nstvout     = 0     ; velocities to output every 25000 steps
nstenergy   = 1000      ; save energies every 2 ps
nstlog      = 1000      ; update log file every 2 ps
nstxtcout   = 10000         ; suppress (tlumic) xtc trajectory
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
cutoff-scheme    = Verlet
verlet-buffer-drift = 0.005
ns_type     = grid      ; search neighboring grid cells
nstlist     = 20         ; 10 fs
vdwtype     = cut-off
rvdw-switch = 1.0
rlist       = 1.4       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.4       ; short-range electrostatic cutoff (in nm)
rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)
vdw-modifier = Potential-shift
ewald_rtol  = 1e-5      ; relative strenght of the Ewald-shifted potential
rcoulomb
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.12      ; grid spacing for FFT
coulomb-modifier         = Potential-shift
; Temperature coupling is on
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc_grps     = System                ; two coupling groups - more accurate
tau_t       = 0.1                           ; time constant, in ps
ref_t       = 298                           ; reference temperature, one
for each group, in K
; Pressure coupling is on
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
nstcalclr = 1     ;period between calculations of long-range every step


Let me know if you see something wrong please. It seems it works well.

Steven