[gmx-users] Problem with g_dipoles and SPCE water

[Tom Kirchner]

On 04/10/2012 11:10 AM, gmx-users-request at gromacs.org wrote:
> On 2012-04-10 09:57, David van der Spoel wrote:
>> >  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
> Another point: the literature value of the dielectric constant for SPC/E
> is for the rigid model. Looks like your using a flexible model here.
>
>
>>> >>
>>> >>  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
Thank you for your reply,

I used the rigid model. I also used PME, I think this is the error, for 
g_dipoles seems to be constructed for reaction field. Is this correct?
I'll redo the simulation with reaction field now.

Best
Tom Kirchner
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