AMBER Archive (2006)

Subject: AMBER: Dimer Image Wrapping

From: Melinda Layten (mlayten_at_gmail.com)
Date: Wed Mar 29 2006 - 17:12:00 CST

I'm getting inconsistent results in ptraj trying to get a non-covalently
bonded dimer to center together when stripping water after an explicit
solvent truncated octahedron run.

Sample script:

trajin solvated.x
trajout strip.x nobox

center :1-50 origin
image :51-100 mass
strip :101-9999

go

For a 50 residue monomer. I've tried lots of other combinations, but there
is always some portion of the trajectory where the dimer interface is on the
original box boundary.

This is amber 8.

Ideas?

Melinda Layten

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