question about protein leaving water box

Date: Fri Apr 14 2006 - 21:05:17 CDT


I have just begun using NADM. I have a question about whether I can always
keep the protein in the water box. Will the wrapAll on command guarantee the
protein stay in the water box? The protein reached the edge of the box
between 0.5-1 ns and some part of the protein went out of the protein after
1 ns.
I've read the NAMD user'd guide, but I am not sure I understand clearly what
wrapAll does.

here's the script:

Thank you very much!


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