[gmx-users] Dielectric constant

[Berk Hess]

Hi,

The dielectric constant of your water model will not be 80,
it depends on the water model.
But when you have many ions, the effective dielectric constant
of the water will be lower.

Your mdp parameters are very non-standard.
You should not use a cut-off of 0.7 nm with a grid spacing of 0.12.
I would suggest to use a cut-off of 0.9 nm.

For efficiency you would want to have a time step of 2 fs
and grid search instead of neighbor search.

Or have you done all this because your box is very small?
For such charged systems you need a relatively large box.

Berk

> Date: Wed, 13 Aug 2008 22:48:59 +0530
> From: avinashk.iit.kgp at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Dielectric constant
> 
> 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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