Thanks all for your suggestions so far. I believe I've got things more
or less functional but I want to refine how I'm constructing my
initial simulation box.
In particular, I'm using a custom coarse-grained system, so I'd like
to be able to tailor the effective vdW radii for use with
insert-molecules and solvate commands to accommodate the typically
larger sizes of the CG sites. However, many of my simulations are on
clusters or other resources where I can't edit the vdwradii.dat file
and not all CG particles in my simulation have the same radii, so just
updating the default radius using the -radius option isn't completely
satisfactory either.
Is there a way to tailor these values for each type of CG particle
without editing the database file, or some other similar workaround to
this issue?
Thanks,
Tom
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