[gmx-users] slow speed

[XAvier Periole]

What makes you think it should be so fast?

Nothing appears obviously wrong in the mdp file.

May be this though!

lincs-order              = 12

On Apr 15, 2010, at 4:02 PM, 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.
>    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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