On Tue, Nov 06, 2012, Brown, Kyle wrote:
> I have a large system composed of 6
> monomers. During the course of the trajectory, one of the monomers is
> wrapped to the opposite corner of the periodic box. When performing
> the "two stage" centering/imaging with ptraj as recommended in the
> post, I get what seem to be unreasonable results...
Sounds like a good test case for the "autoimage" command in cpptraj. Have
you tried that? (Be sure your copy of AmberTools12 is up to date, since this
was added as bugfix.16).
Please let us know if this doesn't work, since maybe Dan can then figure out
why, and improve the imaging algorithm.
...dac
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Received on Tue Nov 06 2012 - 12:30:03 PST
