Hi João, Indeed your instinct seems to be good! When switching the Coulomb-Type to Cut-Off, there doesn't seem to be a difference between 4.6 and 4.5. Apparently its an issue with the PME sum. We will investigate further.
Am 24.06.2013 um 14:42 schrieb João M. Damas <jmda...@itqb.unl.pt>: > Niels, > > This is very interesting. At our group, a colleague of mine and I have also > identified differences in the TPI integrator between 4.0.X and 4.5.X, but > we still haven't had the time to report it properly, since we are using a > slightly modified version of the TPI algorithm. > > Instinctively, we were attributing it to some different behaviours in the > RF that are observed between those versions. We also know that the TPI > algorithm began allowing PME treatment from 4.5.X onwards, so maybe there > are some differences going on the electrostatics level? But, IIRC, no > modifications to the TPI code were on the release notes from 4.5.X to > 4.6.X... > > We'll try to find some time to report our findings as soon as possible. > Maybe they are related. > > Best, > João > > > On Mon, Jun 24, 2013 at 10:19 AM, Niels Müller <u...@nielsm.de> wrote: > >> Hi GMX Users, >> >> We are computing the chemical potential of different gas molecules in a >> polymer melt with the tpi integrator. >> The computations are done for CO2 and CH4. >> The previous computations were done with v4.5.5 or 4.5.7 and gave equal >> results. >> >> I recently switched to gromacs version 4.6.1, and the chemical potential >> computed by this version is shifted by a nearly constant factor, which is >> different for the two gas molecules. >> We are perplexed what causes this shift. Was there any change in the new >> version that affects the tpi integration? I will provide the mdp file we >> used below. >> >> The tpi integration is run on basis of the last 10 ns of a 30 ns NVT >> simulation with 'mdrun -rerun'. >> >> Best regards, >> Niels. >> >> ######################### >> The mdp file: >> ######################### >> >> ; VARIOUS PREPROCESSING OPTIONS >> cpp = cpp >> include = >> define = >> >> ; RUN CONTROL PARAMETERS >> integrator = tpi >> ; Start time and timestep in ps >> tinit = 0 >> dt = 0.001 >> nsteps = 1000000 >> ; 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 = 1 >> ; group(s) for center of mass motion removal >> comm-grps = >> >> ; LANGEVIN DYNAMICS OPTIONS >> ; Temperature, friction coefficient (amu/ps) and random seed >> bd-fric = 0.5 >> 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 >> nbfgscorr = 10 >> >> ; OUTPUT CONTROL OPTIONS >> ; Output frequency for coords (x), velocities (v) and forces (f) >> nstxout = 100 >> nstvout = 0 >> nstfout = 0 >> ; Checkpointing helps you continue after crashes >> nstcheckpoint = 100 >> ; Output frequency for energies to log file and energy file >> nstlog = 100 >> nstenergy = 100 >> ; 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 = >> >> ; NEIGHBORSEARCHING PARAMETERS >> ; nblist update frequency >> nstlist = 5 >> ; 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 = 0.9 >> domain-decomposition = no >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> ; Method for doing electrostatics >> coulombtype = pme >> rcoulomb-switch = 0 >> rcoulomb = 0.9 >> ; 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 >> rvdw = 0.9 >> ; Apply long range dispersion corrections for Energy and Pressure >> DispCorr = EnerPres >> ; Extension of the potential lookup tables beyond the cut-off >> table-extension = 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 = 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 = V-rescale >> ; Groups to couple separately >> tc-grps = System >> ; Time constant (ps) and reference temperature (K) >> tau_t = 0.1 >> ref_t = 318 >> ; Pressure coupling >> Pcoupl = Parrinello-Rahman >> Pcoupltype = isotropic >> ; Time constant (ps), compressibility (1/bar) and reference P (bar) >> tau_p = 5.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> ; Random seed for Andersen thermostat >> andersen_seed = 815131 >> >> ; SIMULATED ANNEALING >> ; Type of annealing for each temperature group (no/single/periodic) >> annealing = no >> ; 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 = yes >> gen_temp = 400 >> gen_seed = 1993 >> >> ; OPTIONS FOR BONDS >> ;constraints = none >> constraints = all-bonds >> ; 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 = 1 >> ; 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 >> ; 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-sigma = 0.3 >> >> ; Non-equilibrium MD stuff >> acc-grps = >> accelerate = >> freezegrps = >> freezedim = >> cos-acceleration = 0 >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > João M. Damas > PhD Student > Protein Modelling Group > ITQB-UNL, Oeiras, Portugal > Tel:+351-214469613 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? 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