spoel at xray.bmc.uu.se
Fri Oct 24 21:50:01 CEST 2003
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!)
> 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 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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