Hello All, I am trying to run some calibration calculations with 2/4 fs time steps. I am trying to reproduce the results in the Gromacs 4.0 paper on a protein/water (not the same protein) system with ~100K atoms. I ran 1 ns simulation in the NVE ensemble. My mdp params are shown below. Topolgy was created using -vsite h. My system has 218441 degrees of freedom according to GMXDUMP. My P.E. energy is ~ -1E5 and has not full relaxed after 1ns but is close.
2 fs time step Total Energy 46497.2 36445.6 2630.7 -148.833 -148833 4 fs time step Total Energy 41580.8 37693.4 2856.08 -130.198 -130198 Drift (kt/ns) 2fs/4fs = .34/.29 The drift seems to be much larger for both the 2fs and 4fs time steps then in the paper. Do I have a clear bug in my params? Should I wait till the system fully relaxes before doing the drift calculation? integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.002/0.004 nsteps = 500000/250000 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step = 0 ; mode for center of mass motion removal comm_mode = linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm_grps = system ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10/5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist = 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon-r = 80 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = .9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; 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 = 4 ewald_rtol = 1.e-04 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = no ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 298.0 ; Pressure coupling Pcoupl = No Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.67 compressibility = 4.5e-5 ref_p = 1.01325 ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed = 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 298.0 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = hbonds/all-bonds ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the start configuration continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 6 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 2 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no -- Ilya Chorny Ph.D.
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