[gmx-users] slow speed
Shuangxing Dai
shuangxingdai at gmail.com
Thu Apr 15 16:02:47 CEST 2010
Hi, gmx-users:
I am using latest version of gromacs and found it was really slow. I was
wondering anyone got the same experience and can point out where the problem
is.
I was running double precision for MD. But for each dynamics simulation,
it takes 4 days. I should only take two or three hours.
Here is the .mdp file:
define =
; RUN CONTROL PARAMETERS =
integrator = sd
; start time and timestep in ps =
tinit = 0
dt = 0.001
nsteps = 200000
; number of steps for center of mass motion removal =
nstcomm = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 100
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 100
xtc-precision = 1000
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 50
; ns algorithm (simple or grid) =
ns_type = grid
;OPTIONS FOR PRESSURE COUPLING
Pcoupl = berendsen
tau_p = 1
compressibility = 4.5e-05
ref_p = 0.1
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps = system
tau_t = 0.1
ref_t = 300
; OPTIONS FOR BONDS =
constraints = hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start = no
; Relative tolerance of shake =
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 30
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Ewald
rcoulomb = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-4
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
Can anyone help me? Thank you in advance.
Thanks,
Shuangxing Dai
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