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? 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
