[gmx-users] Re: Energy Drift in Gromacs 4.0

[Ilya Chorny]

Forgot column labels on energies.
                                                         Average       RMSD
    Fluct.      Drift  Tot-Drift2 fs time step Total Energy
 46497.2    36445.6     2630.7   -148.833    -148833
4 fs time step Total Energy                41580.8    37693.4    2856.08
-130.198    -130198

On Tue, Mar 10, 2009 at 7:17 PM, Ilya Chorny <ichorny at gmail.com> wrote:

> Hello All,
> I am trying to run some calibration calculations with 2/4 fs time steps. I
> am trying to reproduce the results in the Gromacs 4.0 paper on a
> protein/water (not the same protein) system with ~100K atoms. I ran 1 ns
> simulation in the NVE ensemble. My mdp params are shown below. Topolgy was
> created using -vsite h. My system has 218441 degrees of freedom according to
> GMXDUMP. My P.E. energy is ~ -1E5 and has not full relaxed after 1ns but is
> close.
>
> 2 fs time step Total Energy                46497.2    36445.6     2630.7
> -148.833    -148833
> 4 fs time step Total Energy                41580.8    37693.4    2856.08
> -130.198    -130198
>
> Drift (kt/ns) 2fs/4fs = .34/.29
>
> The drift seems to be much larger for both the 2fs and 4fs time steps then
> in the paper. Do I have a clear bug in my params? Should I wait till the
> system fully relaxes before doing the drift calculation?
>
>
> integrator               = md
> ; Start time and timestep in ps
> tinit                    = 0
> dt                       = 0.002/0.004
> nsteps                   = 500000/250000
> ; For exact run continuation or redoing part of a run
> ; Part index is updated automatically on checkpointing (keeps files
> separate)
> simulation_part          = 1
> 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                = system
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist                  = 10/5
> ; ns algorithm (simple or grid)
> ns_type                  = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc                      = xyz
> periodic_molecules       = no
> ; nblist cut-off
> rlist                    = 1.0
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype              = PME
> rcoulomb-switch          = 0
> rcoulomb                 = 1.0
> ; Relative dielectric constant for the medium and the reaction field
> epsilon-r                = 80
> epsilon_rf               = 1
> ; Method for doing Van der Waals
> vdw-type                 = Switch
> ; cut-off lengths
> rvdw-switch              = .9
> rvdw                     = 1.0
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                 = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension          = 1
> ; Seperate tables between energy group pairs
> energygrp_table          =
> ; 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               = 1.e-04
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = no
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl                   = no
> ; Groups to couple separately
> tc-grps                  = System
> ; Time constant (ps) and reference temperature (K)
> tau_t                    = 0.1
> ref_t                    = 298.0
> ; Pressure coupling
> Pcoupl                   = No
> Pcoupltype               = Isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p                    = 1.67
> compressibility          = 4.5e-5
> ref_p                    = 1.01325
> ; Scaling of reference coordinates, No, All or COM
> refcoord_scaling         = No
> ; Random seed for Andersen thermostat
> andersen_seed            = 815131
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel                  = yes
> gen_temp                 = 298.0
> gen-seed                 = 173529
> ; OPTIONS FOR BONDS
> constraints              = hbonds/all-bonds
> ; Type of constraint algorithm
> constraint-algorithm     = lincs
> ; Do not constrain the start configuration
> continuation             = no
> ; Use successive overrelaxation to reduce the number of shake iterations
> Shake-SOR                = no
> ; Relative tolerance of shake
> shake-tol                = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order              = 6
> ; 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               = 2
> ; 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
>
>
> --
> Ilya Chorny Ph.D.
>
>


-- 
Ilya Chorny Ph.D.
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