Janne, You may want to look on the GROMACS developers list for a lot of recent discussion relating to energy conservation. It is a fairly complicated issue. http://www.gromacs.org/pipermail/gmx-developers/
David On 4/11/06, Janne Hirvi <[EMAIL PROTECTED]> wrote: > 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 > _______________________________________________ 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
