Dear Amber Mailing List:
I am using AMBER to run md simulations of a 20 residue polypeptide in a TIP3BOX explicit solvent.
I have performed simulations using an initial solvent box of 10.0 Angstroms and also with 15.0 Angstroms.
The non-bonded cutoff I have been using is 9.0 Angstroms.
What affects should I be observing if the solvent box is too small?
I appreciate your guidance. I have had a difficult time finding information about this in the tutorials and in the literature.
Best,
Kristin D. Krantzman
Professor, Chemistry
College of Charleston
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Received on Wed Feb 03 2016 - 09:30:03 PST
