[gmx-users] Tabulated electrostatics not giving expected interactions
Kimberly Bowal
klb83 at cam.ac.uk
Thu Oct 5 13:53:04 CEST 2017
Hello,
I have set up a simple simulation with 1000 water molecules and one K+
ion. The ion is fixed in place at the centre of the box and I expect to
see clustering of the water molecules around the ion over time. Instead I
only see a few weak interactions between one molecule and the ion and am
unsure what is wrong.
I am using a user-defined potential for both VdW and Coulomb interactions
(LJ and point charge) and have included the first lines below (the table
continues until r = 4).
I see in previous posts (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101544.html)
that Gromacs will automatically neutralise a non-neutral system. I
understand why this is done for Ewald methods but does this happen even
with a tabulated Coulomb potential?
Any suggestions as to what am I missing or doing incorrectly here would be
greatly appreciated!
I have attached my key input files as well.
Thank you,
Kimberly
# Parameters for Gromacs table
# Table : A/r^12 - C/r^6 + Dqq/r
# Units in nm kJ/mol
# LJ form
# A 1.144406E-06 C 7.925970E-05
#
# r f( r) = 1/r -f'( r) = 1/r^2 g( r) = -1/r^6 g'( r) = -6/r^7
h( r) = 1/r^12 - h'( r) = 12/r^13
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
5.0000000000E-04 2.0000000000E+03 4.0000000000E+06
-6.4000000000E+19 -7.6800000000E+23 4.0960000000E+39 9.8304000000E+43
1.0000000000E-03 1.0000000000E+03 1.0000000000E+06
-1.0000000000E+18 -6.0000000000E+21 1.0000000000E+36 1.2000000000E+40
1.5000000000E-03 6.6666666667E+02 4.4444444444E+05
-8.7791495199E+16 -3.5116598080E+20 7.7073466293E+33 6.1658773034E+37
2.0000000000E-03 5.0000000000E+02 2.5000000000E+05
-1.5625000000E+16 -4.6875000000E+19 2.4414062500E+32 1.4648437500E+36
2.5000000000E-03 4.0000000000E+02 1.6000000000E+05
-4.0960000000E+15 -9.8304000000E+18 1.6777216000E+31 8.0530636800E+34
-------------- next part --------------
; VARIOUS PREPROCESSING OPTIONS
include =
define =
; RUN CONTROL PARAMETERS
integrator = md-vv
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 1000000
; For exact run continuation or redoing part of a run
init_step = 0
; Part index is updated automatically on checkpointing (keeps files separate) ##added by klb83 (in TT's)
simulation_part = 1
; 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 = ; default is whole syst
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1093
; ENERGY MINIMIZATION and SHELL MD OPTIONS
; Force tolerance and initial step-size
emtol = 1.0
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (1/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 = 1000
nstvout = 1000
nstfout = 1000
; Output frequency for energies to log file and energy file
nstlog = 100
nstcalcenergy = -1
nstenergy = 100
; Output frequency and precision for xtc file
nstxout-compressed = 1000
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
cutoff-scheme = group
nstlist = 1
ns_type = grid
; Periodic boundary conditions:
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 3.0
; long-range cut-off for switched potentials
rlistlong = -1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = User ; cut-off ; PME ; Ewald
; coulomb-modifier = Potential-shift-Verlet ; Potential-shift ; None
rcoulomb_switch = 0.0
rcoulomb = 3.0
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = User ; cut-off ; PME
; vdw-modifier = Potential-shift-Verlet ; Potential-shift ; None
; cut-off lengths
rvdw_switch = 0.0
rvdw = 3.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no ; EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; EWALD/PME/PPPM parameters
; 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
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
; Tables
energygrps = O H K
; Separate tables between energy group pairs
energygrp_table =
; 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 = 3.0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension = -1
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = nose-hoover
nsttcouple = 1
nh-chain-length = 10
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.5
ref_t = 500
; Pressure coupling
Pcoupl = no
Pcoupltype = isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 0.1
compressibility = 4.5e-5
ref_p = 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = no
; SIMULATED ANNEALING
; Type of annealing for each temperature group
annealing = no ; single ; periodic
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 500
gen_seed = 1086
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
continuation = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; 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 = 1
; 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
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall = 0
wall_type = 9-3
wall_r_linpot = -1
wall_atomtype =
wall_density =
wall_ewald_zfac = 3
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = no
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) to energy file
nstorireout = 100
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-power = 0
sc-sigma = 0.3
nstdhdl = 10
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
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