Shuangxing Dai wrote:
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.
How did you establish this benchmark? Are you running in serial or in parallel?
If you're running in parallel, what type of interconnect do the processors
have? If they're high-latency (like gigabit ethernet) you will not get very
good performance.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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