[gmx-users] periodic boundary conditions

[Lianqing Zheng]

What sections? Thanks!


On Thu, 2 Dec 2004, David wrote:

>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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