[gmx-users] Molecular geometry depends on the orientarion

[Anton Feenstra]

"T. Zaraiskaya" wrote:
> 
[..snip..]
>  Note that the upper yellow molecule is the SAME molecule as
>  the lower, it is just rotated 180 around x-axis.
>  Why the results of minimization are different? I can make
>  mdrun to predict the correct conformation of the lower part of the
>  crystal by changing signs of the sugar impropers, but then of course the
>  upper part does not look good. Is it a bug in the program or I am doing
>  something silly?

Did you perhaps mirror the molecule in stead of rotate 180 degrees?
i.e. if you take z=-z, it might look 180 degrees rotated, but is
actually mirrored...

-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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