On Fri, Aug 2, 2013 at 4:48 AM, Trayder <trayder.tho...@monash.edu> wrote: > Hi all, > I've been running an analysis of the same system (protein/ligand/water/ions) > using multiple timesteps (1-5fs) to identify differences in behaviour > between the settings. To do this I've compared the energy outputs of the 5 > simulations, specifically the averages from g_energy and binning the > energies at each step from the log files. > > What I've found is that 1/2/3fs simulations behave nigh identically, as do > 4/5fs. However there is a notable difference between the two groups (graph > linked below). I've additionally matched timestep dependent variables > between simulations to rule out causes such as different coupling > frequencies, the difference was unaffected. > The difference in the Total Energy seems to arise from the Coulomb (SR) and > LJ-SR terms. While the differences are in the order of 0.1% (~170kJ/mol) I > would rest easier being able to explain the sudden change in behaviour from > 3-4fs. > Anyone have any ideas?
Welcome to numerical integration :-) This looks like well-known behaviour (e.g. GROMACS manual 6.7, and refs therein), but it is nice to see it confirmed. Mark > Thanks, > -Trayder > > Binned total energies: > https://docs.google.com/file/d/0By3TeVcanmk8U0EwXzhNYk5JZUk/edit?usp=sharing > > 2fs mdp file: > integrator = md ; simulation algorithm > tinit = 0 > dt = 0.002 > nsteps = 10000000 ; # steps > ; > ; Output Control > nstxout = 500000 ; write coordinates to .trr > nstvout = 500000 ; write velocities to .trr > nstlog = 500 ; write energies to .log > nstenergy = 500 ; write energies to .edr > nstxtcout = 8000 ; write coordinates to .xtc > energygrps = Protein OLAT Water_and_Ions ; > ; > ; Neighbour Searching > nstlist = 10 ; update neighbour list > ns_type = grid ; neighbour list method > pbc = xyz ; periodic boundary > conditions > rlist = 0.9 ; cut-off for short-range > neighbour (nm) > cutoff-scheme = verlet > ; > ; Electrostatics and VdW > coulombtype = PME ; type of coulomb > interaction > rcoulomb = 0.9 ; cut-off distance for > coulomb > epsilon_r = 1 ; dielectric constant > rvdw = 0.9 ; cut-off for vdw > fourierspacing = 0.12 ; maximum grid spacing for > FFT > pme_order = 4 ; interpolation order for > PME > ewald_rtol = 1e-5 ; relative strength of > Ewald-shifted > DispCorr = EnerPres ; long range dispersion > corrections > ; > ; Temperature Coupling > Tcoupl = v-rescale ; type of temperature > coupling > tc-grps = Protein non-Protein ; coupled > groups > tau_t = .1 .1 ; T-coupling time constant > (ps) > ref_t = 310 310 ; reference temperature (K) > ; > ; Pressure Coupling > Pcoupl = parrinello-rahman ; type of pressure > coupling > Pcoupltype = isotropic ; pressure coupling geometry > tau_p = 2.0 ; p-coupling time constant > (ps) > compressibility = 4.5e-5 ; compressibiity > ref_p = 1.0 ; reference pressure (bar) > ; > ; Velocity Generation > gen_vel = no ; generate initial > velocities > ; > ; Bonds > constraints = all-bonds ; which bonds to contrain > constraint_algorithm = lincs ; algorithm to use > lincs_order = 4 > lincs_iter = 2 > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Trying-to-explain-differences-in-behaviour-between-2fs-and-5fs-timesteps-tp5010304.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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
