[gmx-users] Molecular geometry depends on the orientarion
tz at disco.physics.uoguelph.ca
Wed Jul 10 23:46:04 CEST 2002
I am simulating Galactosyl Ceramide lipid bilayer using
ffG43a2x ff. I've built the topology and as a first test
I am simulating the crystal of this lipid.
Surprisingly, when I performed energy minimization it turned out
that the optimized molecular geometry depends on the orientation of the
I have attached the picture, showing experimental X-ray
structure (yellow) and optimized structure (red).
As you can see, for the upper molecule deviation between the
experimental and minimized coordinates is rather small and sugar
impropers are reproduced correctly. However, the lower part of the
crystal looks as if all sugar impropers would have changed their sign.
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
University of Guelph
Guelph, ON, N1G 2W1
email:tz at helios.physics.uoguelph.ca
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