[gmx-users] g_sorient HELP!!!

Berk Hess gmx3 at hotmail.com
Thu Oct 30 09:58:01 CET 2003

>If I put the water molecule at a distance greater than .5 nm I still get
>one peak at 135 degrees.

My guess is that the problem is the box.
In the gro file you mailed to the list, there was no box.
If you use this file gromacs might generate a incorrect box.
I still only get one peak though and never at 135 degrees.
But maybe you have used a different box size.
g_sorient calculates the smallest distance using periodic
boundary conditions. So it could be that it uses an image
which is displaced in the y-direction. This answer could
(correctly) be 135 degrees.
The solution is then to use a very large box.


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