> So my question is this: Is there anyway to speed-up this start up time,
> or at the very least a way to perform consecutive minimizations without a
> startup in between every one?
Keep in mind the "startup" involves assigning the molecular mechanics atom/bond
types, assigning aromaticity, detecting rings, etc. Molecules with large
numbers of fused aromatic rings are challenging for the current aromaticity
code in Open Babel, and so this "startup time" is highly dependent on the size
and complexity of the molecule.
You can, of course, perform a variety of MM calculations consecutively without
penalty using code in Python or C++ -- for example, the "--gen3d" flag for
obabel will generate initial coordinates, followed by a steepest-descent
search, a conformer search, and a conjugate gradient optimization of the final
conformation. All these are done without needing to hit "startup" again.
Unless you have an extremely slow disk, or extremely limited RAM, the actual
startup of "obminimize" or other programs should be fractions of a second. You
can test this by trying to minimize something like benzene.
Hope that helps,
-Geoff
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