Niels, Which force-field did you use? I guess an uncharged CH4 shouldn't be giving different results for TPI when changing coulomb... Actually, coulomb is turned off if there's no charge in the particles to insert, if I remember the code correctly.
João On Mon, Jun 24, 2013 at 3:40 PM, Niels Müller <u...@nielsm.de> wrote: > 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? 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
