[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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