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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