[gmx-users] why it is so slow

[Albert]

hello:

  I am running a 40ns REMD with GBSA solvent NPT simulations. It is 
exchange for 16 different temperature with exchange step 300.

mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s 
remd_.tpr -multi 16 -replex 300


I found that it will require 1 months to be finished which is a really 
long time.

I am just wondering is there anything I did wrong for the .mdp so that 
it is so slow? here is my .mdp file.

thank you very much





title = Protein-ligand complex NPT equilibration
; Run parameters
integrator = sd ;
nsteps = 20000000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
nstxout = 0 ; save coordinates every 0.2 ps
nstvout = 0 ; save velocities every 0.2 ps
nstfout = 0

nstxtcout = 500
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 1000 ; update log file every 0.2 ps
energygrps = Protein_LIG
; 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 = simple ; search neighboring grid cells
nstlist = 0 ; 10 fs
rlist = 0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0 ; short-range electrostatic cutoff (in nm)
rvdw = 0 ; short-range van der Waals cutoff (in nm)

; Electrostatics
coulombtype = cutoff ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.15 ; grid spacing for FFT

; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_LIG  ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 310 ; reference temperature, one for each group, in K

; Pressure coupling
pcoupl = no    ; pressure coupling is on for NPT
; Periodic boundary conditions
; Pressure coupling
pcoupl = no    ; pressure coupling is on for NPT
; Periodic boundary conditions
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
pbc=no
; Dispersion correction
DispCorr = no ; account for cut-off vdW scheme
pcoupltype  = isotropic                     ; uniform scaling of box vectors
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 310 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
ld_seed=-1

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = GBSA
comm_mode = ANGULAR

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension = 2.25936