[gmx-users] Energy Conservation with 4fs timestep

[Joe Joe]

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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