[gmx-users] periodic boundary conditions

[David]

On Thu, 2004-12-02 at 10:31 -0500, Lianqing Zheng wrote:
> Dear GMX-pals,
> 
> I have questions on how Gromacs deals with PBC for molecules. For example, 
> for a water molecule H1-O-H2 with only H2 out of simulation box, if H2 is
> moved back to the box by periodic boundary conditions, then the O-H2
> bonded will be distorted. How does Gromacs deal with this?
> 
chpater 3 and 4 in the manual
> Thanks a lot!
> 
> Lianqing
> 
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-- 
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://xray.bmc.uu.se/~spoel
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