[gmx-users] Energy Drift in Gromacs 4.0
Ilya Chorny
ichorny at gmail.com
Wed Mar 11 03:17:16 CET 2009
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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