[gmx-users] calculating dielectric constant

[David van der Spoel]

Qiao Baofu wrote:
> Hi David,
> Thanks for your kindly reply.
> Because I am simulating a pure fluid system, I used the epsilon-r = 1in 
> the .mdp file.
> _____________________________________________________
> coulombtype              = pme
> rcoulomb-switch          = 0
> rcoulomb                 = 1.1
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon-r                = 1
> _____________________________________________________
> 
>  If I don't use the Reaction-Field method, how should I use the 
> -rpsilonRF option? (I want to use 0. But because 0 means infinity here, 
> I have no idea how to use it)  I calculated dielectric constant with and 
> without "-esilonRF" option, please see the following results
> _____________________________________________________
> g_dipoles -temp 425 -f md2 -s md2 -enx md2.edr
> Epsilon = 826.496
> 
> g_dipoles -temp 425 -epsilonRF 1 -f md2 -s md2 -enx md2.edr
> Epsilon = -2.01094
> _____________________________________________________
> 
> Neither result are the values what I expect. What wrong?
> 
> 
The option you pass to g_dipoles should match what you use for 
epsilon_surface (PME) or epsilon_rf (RF) in the MD simulation. Since you 
have done the MD with epsilon_surf = 0 (infinite) you can not use 1 for 
the analysis. The high number that you get is probably because of the 
high temperature. Was the simulation also done at this T? Which liquid 
is this?

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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