From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Fri Jun 18 2004 - 07:04:58 CDT
Hi all,
Are there any methods available within namd or some other auxillary program to
recenter your protein back into the waterbox. I have a protein of 750
residues that tends to move outside the waterbox after 2 ns of md simulation
using the NPT ensemble. The waterbox is already large enough with total
system size 90 k atoms and 26421 water molecules. Is there a reasonable way
to center the protein back in the box so I could contibue my simulation.
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