[gmx-users] slow speed

[Justin A. Lemkul]

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
> 

-- 
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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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