[gmx-users] g_dipoles questions

David van der Spoel spoel at xray.bmc.uu.se
Wed Dec 24 17:01:38 CET 2008

Semen Esilevsky wrote:
> Dear David,
> Thank you for reply! However there are still some question:
>>> Dear All,
>>> I have few questions about g_dipoles, which are not explained in the manual:
>>> 1) What method is used to calculate the epsilon? Is there a reference which can be cited? Is it suitable for water solutions?
>> In principle it is suitable for solutions of neutral molecules only. 
> So, it should work for SPC water for example? 

> I'm confused by the phrase in the man page "you can compute e.g. the dielectric constant for low dielectric media". What is "low"? Does it mean that  the method works for, say, benzene but not for water?

anything of neutral molecules.

>> The references are to Neuman papers from the 1980s.
> Could you please give a little bit more detailed citation? Neuman is a widespread name and 1980s is 10 years... At least a title or some keywords are needed to find these papers.
check my 1998 JCP paper, the ref is given in g_dipoles.
> Sincerely,
> Semen
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David van der Spoel, PhD, Professor of Biology
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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