system splitted

From: lecan (
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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