[gmx-users] Problem with g_dipoles and SPCE water

Tom Kirchner tomkirch at mis.mpg.de
Tue Apr 10 09:43:35 CEST 2012

```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.

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

#==========================================

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

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