moving out of the box

From: Ariel Talavera Perez (
Date: Thu Feb 13 2014 - 09:57:16 CST


I just ran 0.5 us MD us of a protein dimer in complex with DNA in a
water box. Unfortunately I did not restrain the neither the translation
nor the rotation of the complex. In several frames part of the complex
moved out of the water box. This makes that sometimes one of the
monomers is gone from the water box, and the same monomer but from the
neighbour cell appears.
Is there anyway to fix this issue for the MD I already ran? I mean, how
can I get the "right" complex in all the frames?

Thanks a lot in advanced


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