It's been asked before, but I've been contemplating my next career moves
and a number of problems in materials science would be a lot easier to do
with Amber if it could simulate systems in which bonded structures could
extend infinitely. Having implemented the functionality in mdgx, I would
say that, in principle, the only thing that needs to change in PMEMD /
sander to have a bond traverse the box imaging would be to import the box
dimensions, make appropriate copies of the coordinates, then transform and
image the copies to compute forces and energies.
Any objections if I take this on? Might be something nice to do early in a
cycle, so there can be lots of testing before the next release. Can anyone
suggest things I might break if I try this?
Thanks,
Dave
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Received on Wed Apr 06 2016 - 14:00:03 PDT
