[gmx-users] g_dipoles and fluctuation of the total dipolemoment

[David van der Spoel]

Guido Humpert wrote:
> Hello again,
> 
> Thanks for your responses and suggestions.
> I think I understood the way epsilon is calculated in the source code,
> although I'm not very fermiliar with C.
> My question now is about your best bet of simulating the peptides in
> different concentration of water.
> What kind of simulation would be best in this case? My fist guess would
> be a md with RF, as in the Gromacs paper (1998). Is it possible to
> transfer the conditions of a system of water to a system of a peptide in
> water?
> What's the difference between an extrapolation to zero water
> concentration and the simulation of a peptide without water?
> 
You can try it without water, however you should avoid having vacuum in 
the system, so you probably want to fill a box with multiple peptides. 
Do also make sure that the system still is liquid. Convergence will be 
very slow however, and I doubt that it is realistic to have completely 
dehydrated peptides.

Do not use RF, use PME instead.



-- 
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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