Thanks for your response David! I tried to simulate bulk water (1372 SPC/E molecules) with your parameters and observed same kind of problems with energy conservation as with my earlier parameters (rlist=rvdw=rcoulomb=1.2 & nstlist=10). In single precision NVE simulation (500ps) drift in total energy was +1828.88kJ/mol with your parameters and +1861.13kJ/mol with mine. So I am little bit confused and I still have couple of questions:
1) Are this large drifts normal or have I done something stupid? I mean have you observed this kind of artifacts as well? Atleast from the next mail I would think that better energy conservation should be achieved with your parameters? http://www.gromacs.org/pipermail/gmx-users/2002-December/003510.html 2) I still dont understand why parameter combination rlist>rcoulomb with PME conserves total energy almost completely, but however I should use parameters so that rlist=rcoulomb. Can you comment on this because Berk may have noted your request or then he have had no time to do that? Or is it so trivial that I should find explanation from some trivial text book? Thanks, Janne > Janne Hirvi wrote: > > Hello David! > > > > I read your interesting new article "The Origin of Layer Structure > Artifacts in > > Simulations of Liquid Water" and I would like to know especially what kind > of > > NS parameters you have used in the simulations with PME and are the > following > > parameters correct otherwise? > > > > dt=0.002 > > nstlist=5 > > rlist=? > > coulombtype=PME > > rcoulomb=0.9 > > vdwtype=cut-off > > rvdw=? > I'm attaching my mdp file. > > We have just disabled the option to have rlist != rcoulomb with PME. > > > > > I am interested especially about the rlist parameter because there seems to > be > > some energy conservation problems in my water simulations. At least I > couldn't > > achieve energy conservation with single precision complilation and with > > double precision compilation energy is conserved only when switch(shift?) > > function is used for vdw interactions (rlist>rvdw>rvdw_switch) and PME for > > coulombic interactions (rlist>rcoulomb). If rlist is equal to rcoulomb I > need > > to update NS list at every time step but with preceding parameters energy > is > > conserved even when nstlist=10. > > > > So should I use rlist>rcoulomb with PME when nstlist>1 to take into > account > > movement of atoms/molecules(charge groups) near the real space cut-off > limit > > (rcoulomb) or is there something I don't understand? Atleast from the > manual > > someone could get the picture that rlist should be equal to rcoulomb and > there > > are also different kind of opinions on mailing list? > > Maybe Berk can comment? > > > > > > > Thanks for any comments in advance! > > > > Janne > > > > > ------------------------------------------------------------------------------ > > Janne Hirvi, MSc(Physical Chemistry), Researcher > > University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, > FI > > Tel: +358 13 2514544 & +358 50 3474223 > > E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED] > > > ------------------------------------------------------------------------------ > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > -------------- next part -------------- > ; > ; File 'mdout.mdp' was generated > ; By user: spoel (291) > ; On host: matisse > ; At date: Sun Aug 11 22:20:40 2002 > ; > > ; VARIOUS PREPROCESSING OPTIONS = > title = > cpp = /lib/cpp > > ; RUN CONTROL PARAMETERS = > integrator = md > ; start time and timestep in ps = > tinit = 0 > dt = 0.002 > nsteps = 1000000 > ; 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 = > > ; LANGEVIN DYNAMICS OPTIONS = > ; Temperature, friction coefficient (amu/ps) and random seed = > bd-temp = 300 > bd-fric = 0 > ld-seed = 1993 > > ; ENERGY MINIMIZATION OPTIONS = > ; Force tolerance and initial step-size = > emtol = 100 > emstep = 0.01 > ; Max number of iterations in relax_shells = > niter = 20 > ; Step size (1/ps^2) for minimization of flexible constraints = > fcstep = 0 > ; Frequency of steepest descents steps when doing CG = > nstcgsteep = 1000 > > ; 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 = 1000 > nstenergy = 100 > ; Output frequency and precision for xtc file = > nstxtcout = 250 > 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 = > > ; NEIGHBORSEARCHING PARAMETERS = > ; nblist update frequency = > nstlist = 5 > ; ns algorithm (simple or grid) = > ns-type = Grid > ; Periodic boundary conditions: xyz or no = > pbc = xyz > ; nblist cut-off = > domain-decomposition = no > > ; OPTIONS FOR ELECTROSTATICS AND VDW = > ; Method for doing electrostatics = > coulombtype = PME > rcoulomb-switch = 0 > ; Dielectric constant (DC) for cut-off or DC of reaction field = > epsilon-r = 1 > ; Method for doing Van der Waals = > vdw-type = Cut-off > ; cut-off lengths = > rvdw-switch = 0 > ; Apply long range dispersion corrections for Energy and Pressure = > DispCorr = Ener > ; 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 = 1e-05 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = no > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS = > ; Temperature coupling = > tcoupl = Berendsen > ; Groups to couple separately = > tc-grps = System > ; Time constant (ps) and reference temperature (K) = > tau-t = 0.1 > ref-t = 298.15 > ; Pressure coupling = > Pcoupl = Berendsen > Pcoupltype = Isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) = > tau-p = 1.0 > compressibility = 5e-5 > ref-p = 1 > > ; SIMULATED ANNEALING CONTROL = > annealing = no > ; Time at which temperature should be zero (ps) = > zero-temp_time = 0 > > ; GENERATE VELOCITIES FOR STARTUP RUN = > gen-vel = yes > gen-temp = 300 > gen-seed = 173529 > > ; OPTIONS FOR BONDS = > constraints = none > ; Type of constraint algorithm = > constraint-algorithm = shake > ; 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 > ; 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) to energy file = > nstorireout = 100 > > ; Free energy control stuff = > free-energy = no > init-lambda = 0 > delta-lambda = 0 > sc-alpha = 0 > sc-sigma = 0.3 > > ; Non-equilibrium MD stuff = > acc-grps = > accelerate = > freezegrps = > freezedim = > cos-acceleration = 0 > > ; 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 > rlist = 0.9 > rcoulomb = 0.9 > rvdw = 0.9 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php