[gmx-users] Problem with g_dipoles and SPCE water

[David van der Spoel]

On 2012-04-10 11:16, Tom Kirchner wrote:
> 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
>
>
No! g_dipoles does not care. You may have a remnant command in your mdp 
file (-DFLEXIBLE), please remove it. For  rigid model there should not 
be any fluctations in the dipole.

-- 
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