[gmx-users] Trying to explain differences in behaviour between 2fs and 5fs timesteps

[Mark Abraham]

On Fri, Aug 2, 2013 at 4:48 AM, Trayder <trayder.thomas at 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.
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