[gmx-users] Problem with g_dipoles and SPCE water
David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 10 09:57:26 CEST 2012
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
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
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