[gmx-users] g_dipoles questions

[David van der Spoel]

Semen Esilevsky wrote:
> 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. The 
references are to Neuman papers from the 1980s.


> 2) I can't figure out the purpose of the option -enx. When I supply edr 
> file with this option the value of epsilon changes slightly and options 
When you supply the edr file, the trajectory is not read anymore. The 
idea is that one often saves the energy file more often than the trajectory.


> -slab and -d stop working. Option -d makes no effect at all, the file 
> dipdist.xvg does not appear. With -slab the resulting file slab.xvg 
> always contains zeros regardless of the system. Without -enx these 
> options work as expected. What is the reason of these weird side 
> effects? Is this a bug or a feature?
> 3) Many options are undocumented at all (-adip, -dip3d, -cmap, -q, 
> -slab). It is easy to deduce what -slab does, but what on earth is -adip 
> or -cmap?

Hm, as always just try it... use xpm2ps to make nice plots. These give 
dipole distribution in 2D or 3D.


> 
> Thanks in advance!
> 
> Semen
> 
> 
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se