[gmx-users] g_sorient

[David]

On Fri, 2003-10-24 at 01:27, Ilya Chorny wrote:
> How does one compile just the tools like g_sas or g_sorient?
> 
you stil have to compile gmxlib and mdlib, so might as well install the
whole thing (but in another directory!)

> Ilya
> 
> On Wed, 2003-10-22 at 12:53, Ilya Chorny wrote:
> > Hello,
> > 
> > I am trying to use g_sorient to calculate the solvent orientation around
> > my solute. To test g_sorient I created a gro file the has one Atom and
> > one H2O molecule in  the following orientation.
> > 
> >          H
> > A --- O
> >          H
> > 
> > When I look at the output files for I see a distribution for theta 1
> > peaked at 90 degrees and a distribution for theta 2 peaked at 90
> > degrees. Three question: 1.) Why do I see a distribution? I would expect
> > only one point. 2.) Why is theta 1 peaked at 90 degrees? Based on the
> > definition in the manual it should be either 0 or Pi. 3.) Does g_sorient
> > normalize the angles.
> > 
> > Thanks
> > 
> > 
> > Ilya
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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