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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
