Greetings Gromacs Users, I have run single precision isothermal-isobaric ensemble simulations using particle mesh Ewald (PME) (in Gromacs 4.0.5) and compared the results to those of (what I think should be) equivalent single precision simulations using the classic implementation of Ewald. The systems under study are binary mixtures of methanol + water at 300 K and 1 bar across the full composition range. The classic Ewald simulations have a more negative total potential energy (PE) for each composition, with the difference increasing as the mole fraction of methanol increases. The reduced PE differences, (<PME total PE> - <Ewald total PE>)/RT (angled brackets denote time averages), range between 0.29 for pure water and 0.93 for pure methanol. When starting an Ewald simulation from a structure that was equilibrated with PME, convergence to the more negative (incorrect) Ewald potential energy takes place within approximately twenty picoseconds. The box volume also decreases in the classic Ewald simulations e.g., to 81% of its original volume in the equimolar methanol + water composition. A test of the number of lattice vectors used in the simulations shows that the results are converged. All the simulations employ the Nose-Hoover thermostat and the Parrinello-Rahman barostat.
Canonical ensemble classic Ewald simulations do however reproduce the canonical and isothermal-isobaric PME average total PE, however the pressure is incorrect, averaging ~-5,000 bar. Below my message, please find the mdp file used in the classic Ewald simulations. The only differences between the mdp file below and that used in the PME simulations are the following lines: coulombtype = PME fourierspacing = 0.12 Is it possible that the pressure tensor is incorrect in the classic Ewald code? Sincerely, Elizabeth Ploetz ; ; File 'mdout.mdp' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Dec 23 12:23:42 2008 ; ; VARIOUS PREPROCESSING OPTIONS title = ; Preprocessor - specify a full path if necessary. cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 10000 dt = 0.002 nsteps = 500000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 500 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 10 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 500 nstvout = 500 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint = 5000 ; Output frequency for energies to log file and energy file nstlog = 500 nstenergy = 500 ; Output frequency and precision for xtc file nstxtcout = 0 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = MOH SOL ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.5 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Ewald rcoulomb-switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon-r = 1.0 epsilon_rf = 1.0 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; 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 = 0.6 ; 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 = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = Nose-Hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau-t = 0.1 ref-t = 300.0 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 0.5 compressibility = 4.5e-5 ref-p = 1 ; Random seed for Andersen thermostat andersen_seed = 829473 ; OPTIONS FOR QMMM calculations QMMM = no ; Groups treated Quantum Mechanically QMMM-grps = ; QM method QMmethod = ; QMMM scheme QMMMscheme = normal ; QM basisset QMbasis = ; QM charge QMcharge = ; QM multiplicity QMmult = ; Surface Hopping SH = ; CAS space options CASorbitals = CASelectrons = SAon = SAoff = SAsteps = ; Scale factor for MM charges MMChargeScaleFactor = 1 ; Optimization of QM subsystem bOPT = bTS = ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 300.0 gen-seed = 173520 ; OPTIONS FOR BONDS constraints = all-bonds ;constraints = none ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; 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 = 4 ; 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 ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file nstdisreout = 100 ; Orientation restraints: No or Yes orire = no ; Orientation restraints force constant and tau for time averaging orire-fc = 0 orire-tau = 0 orire-fitgrp = ; Output frequency for trace(SD) and S to energy file nstorireout = 100 ; Dihedral angle restraints: No, Simple or Ensemble dihre = No dihre-fc = 1000 dihre-tau = 0 ; Output frequency for dihedral values to energy file nstdihreout = 100 ; Free energy control stuff free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 deform = ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E-x = E-xt = E-y = E-yt = E-z = E-zt = ; User defined thingies user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! 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