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

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 3 17:31:36 CEST 2006

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 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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