[gmx-users] Problem with g_dipoles and SPCE water

[David van der Spoel]

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
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