Hello all,
This is somewhat a basic question: in any protein simulation, when using a
solvate box with a certain cutoff, such as 12 angstroms, tleap adds water
padding of 12 angstroms in all directions. However, the box generated will
be a cuboid. During simulation, the protein can rotate and align
perpendicularly to its starting orientation. If the protein is somewhat
like a stretched ellipsoid shaped rather than round or globe-like, this
rotation could destroy the 12 angstrom padding (in other dimensions) that
we used for the construction of the cuboid. Also, during simulation, there
is a chance that the rotation can make the protein interact with its own
image in smaller dimension axes. In that case, why is the cuboid box
required as an option to generate periodic boxes?
with regards,
--
*MIDHUN K MADHU*
Ph.D Student
Dept. of Biological Sciences
IISER Bhopal
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Received on Fri Sep 22 2023 - 06:30:02 PDT
