[gmx-users] Dielectric Constant

[Life Sciences Inc]

Hi

I am getting the value of Epsilon from the output of gmx dipoles as
approximately close to 60, in my mdp file I used the default parameters for
epsilon-r (1) and for epsilon-rf(0), the output as below

Select a group: 12
Selected 12: 'Water'
There are 4531 molecules in the selection
Last frame      50000 time 100000.000
Average volume over run is 149.579

Dipole moment (Debye)
 ---------------------
Average  =   2.2740  Std. Dev. =   0.0001  Error =   0.0000

The following averages for the complete trajectory have been calculated:

Total < M_x > = 3.03347 Debye
Total < M_y > = -12.361 Debye
Total < M_z > = -19.1034 Debye

Total < M_x^2 > = 28871.2 Debye^2
Total < M_y^2 > = 29326.8 Debye^2
Total < M_z^2 > = 29241.6 Debye^2

Total < |M|^2 > = 87439.6 Debye^2
Total |< M >|^2 = 526.935 Debye^2

< |M|^2 > - |< M >|^2 = 86912.7 Debye^2

Finite system Kirkwood g factor G_k = 3.7096

Infinite system Kirkwood g factor g_k = 2.49376

Epsilon = 59.7615


But I want to calculate the dielectric constant with the imaginary surface
around my system or it can also be said as with PBC boundaries, for which
there is an option in gromacs for mdp file which is epsilon-surface(0), but
whenever I am using this option with other than default value with
epsilon-r = 1 or epsilon-rf = 0 or epsilon-r = 1 or epsilon-rf = 1,  I am
getting LINCs error. For electrostatistics I am using PME. As I have used
SPC water model I tried to use the value of epsilon-surface = 70, and also
used 60 so that these values may correct the lincs error. I have also made
my input molecule as a whole using gromacs. Simulation runs if I use
epsilon-surface = 0 but other than this simulation i not running. I am
using gromacs version 5.

I am not getting where is the problem and how it can be solved.

Kindly help.

On Thu, Jun 16, 2016 at 10:05 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> These are all documented in the mdp sections. What isn't clear?
>
> Mark
>
> On Thu, 16 Jun 2016 18:06 Life Sciences Inc <
> contact.lifesciences.inc at gmail.com> wrote:
>
> > Hi all
> >
> > Exactly in Gromacs what and where is Dielectric constant option , If for
> > example I have to run simulations to study behavior of water around
> > molecules, and I am using experimental value of SPC/E water model as 71
> for
> > Dielectric constant. But in my input file for gromacs where I will put
> > Dielectric constant is it epsilon-surface, or epsilon-r or epsisilon-rf,
> it
> > is little confusing. Kindly someone elaborate .
> >
> > Thank you
> > --
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