[gmx-users] Dielectric constant
avinash kumar
avinashk.iit.kgp at gmail.com
Wed Aug 13 19:18:59 CEST 2008
Dear users,
I am trying to simulate electroosmotic flow using GROMACS.
The liquid is water and I am trying to find the dielectric constant of
water. I am just getting a value of dielectric constant of 10. i am
expecting 80 for water. I am attaching my mdp . I would be grateful if
somebody points some mistake.
title = md
cpp = cpp
include = -I../top
define =
integrator = md
tinit = 0
dt = 0.001
nsteps = 700000
init_step = 0
comm-mode = Linear
nstcomm = 500
comm-grps =
bd-fric = 0
ld-seed = 1993
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
nstxout = 100
nstvout = 100
nstfout = 100
nstcheckpoint = 20
nstlog = 100
nstenergy = 10
nstxtcout = 0
xtc-precision = 1000
xtc-grps =
energygrps = WA WA1 WA2 SOL NA+
nstlist = 10
ns_type = simple
pbc = xyz
rlist = 0.7
domain-decomposition = no
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 0.7
epsilon_r = 1
epsilon_rf = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 0.7
DispCorr = No
table-extension = 1
energygrp_table =
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3dc
epsilon_surface = 0
optimize_fft = no
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
tcoupl = Berendsen
tc-grps = WA WA1 WA2 SOL NA+
tau_t = 0.1 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300 300
Pcoupl = No
Pcoupltype = Isotropic
tau-p = 1
compressibility =
ref-p =
andersen_seed = 81513
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = no
Shake-SOR = no
shake-tol = 1e-04
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
disre = No
disre-weighting = Conservative
disre-mixed = no
disre-fc = 1000
disre-tau = 0
nstdisreout = 100
orire = no
orire-fc = 0
orire-tau = 0
orire-fitgrp =
nstorireout = 100
dihre = No
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-power = 1
sc-sigma = 0.3
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps = WA WA1 WA2
freezedim = y y y y y y y y y
cos-acceleration = 0
deform =
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E_x = 1 0.1 0
E-xt =
E-y =
E-yt =
E-z =
E-zt =
--
Avinash Kumar.
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