[gmx-users] Energy Conservation with 4fs timestep
Joe Joe
ilchorny at gmail.com
Wed Apr 1 03:37:06 CEST 2009
Hi,
I get good conservation when running NVE in gromacs with 4 fs when I use
PME-switch for electrostatics but not so good when I use switch. Any
thoughts why that would be? Params shown below.
Thanks,
Ilya
;
; File 'mdout.mdp' was generated
; By user: ichorny (502)
; On host: master.simprota.com
; At date: Tue Mar 31 18:01:39 2009
;
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include =
; e.g.: -DI_Want_Cookies -DMe_Too
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.004
nsteps = 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
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100000
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 10
nstenergy = 10
; Output frequency and precision for xtc file
nstxtcout = 5000
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 1.1
; OPTIONS FOR ELECTROSTATICS AND VDW; Method for doing electrostatics
coulombtype = pme-switch
rcoulomb-switch = .85
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 = .85
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-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension = 2.092
; 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
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