From: lecan (lecan_at_ibt.unam.mx)
Date: Fri Mar 02 2012 - 06:54:50 CST
Hi everybody.
I am trying to minimize and MD simulate a protein in a water box with
ions added with Meadionize plugin for VMD and charmm parameters. It
minimizes to the end of the process apparently without trouble. At the
first frame everything look OK, but at the second frame protein and
water box split at the middle and move apart (is a dimeric protein). A
part of each half of the protein moves out the half water box in which
it is immersed and the connectivities of some residues are wrong. I have
tried with a bigger water box, with the same result. Can anybody can
give a light on this problem?
Thank you in advance,
Luis L.
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