[gmx-users] Problem with g_dipoles and SPCE water

[David van der Spoel]

On 2012-04-10 09:43, Tom Kirchner wrote:
> Hi all,
>
> I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E
> water. Sadly the result for the dielectric constant (e_sim=109.713)
> looks very different from experimental (e_exp=78) and reported values
> for SPCE (e_paper=70). I put the command line and the output below.

Did you run the simulation with PME or at the very least RF?

>
> Gromacs 4.5.3, SPC/E water, 20ns, NPT, 300K, 1bar
>
> g_dipoles -corr total -c dipoles -f md_20ns.xtc -s md_20ns.tpr -b 0 -e 20000
You don't need the corr flag for computing the dielectric constant.

>
> #==========================================
>
> Using 5 as mu_max and -1 as the dipole moment.
> WARNING: EpsilonRF = 0.0, this really means EpsilonRF = infinity
> Selected 0: 'System'
> There are 1024 molecules in the selection
> Using Volume from topology: 30.2049 nm3
> Average volume over run is 30.2103
> t0 0, t 20000, teller 10001
>
> Dipole moment (Debye)
> ---------------------
> Average  =   2.4883  Std. Dev. =   0.1342  Error =   0.0000
>
> The following averages for the complete trajectory have been calculated:
>
>    Total<  M_x>  = 1.45986 Debye
>    Total<  M_y>  = 5.71202 Debye
>    Total<  M_z>  = 3.39196 Debye
>
>    Total<  M_x2  >  = 10964.8 Debye2
>    Total<  M_y2  >  = 10794.4 Debye2
>    Total<  M_z2  >  = 10762.4 Debye2
>
>    Total<  |M|^2>  = 32521.6 Debye2
>    Total |<  M>|^2 = 46.2638 Debye2
>
> <  |M|^2>  - |<  M>|^2 = 32475.4 Debye2
>
> Finite system Kirkwood g factor G_k = 5.12208
> Infinite system Kirkwood g factor g_k = 3.43028
>
> Epsilon = 109.713
>
> #==========================================
>
> I would be really grateful if anybody could point me to my error. I
> attached my .mdp file in case the error lies there.
>
> Best regards
> Tom
>
>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se