Problem with water box

From: ramya wwjd (
Date: Fri Mar 02 2007 - 06:50:26 CST

Dear namd users,
                         I am a bit confused about how to create waterbox
for my protein.My problem is my protein is large of about 574 residue than
ubiquitin.In the namd tutorial the dimension of waterbox for ubiquitin is
given as 5 A. wheather this dimension value for ubiquitin is approximate or
accurate? if it is accurate how to calculate the dimension can you explain
me in detail. I used same dimension value(5A) for my protein & I run the
simulation for water box, where the protein came out of the
waterbox.watingfor your positive reply.
Thank you

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