[gmx-users] Energy Drift in Gromacs 4.0

[Ilya Chorny]

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.
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