AMBER Archive (2007)

Subject: AMBER: PME and counter ions

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Tue Dec 18 2007 - 10:04:12 CST

Dear Amber users,

We are simulating a protein of ~7500 residues using PME with pmemd. It
is quite negatively charged, so we added ~250 counter ions (Na+) with
the Leap (function addIons). The protein is really unstable, which is
not what we expected. We suspect that this is due to counter ions
interacting to certain places in the protein.

Anyway, earlier posts suggests (and/or recommends?) to use plasma
instead of explicit counter ions. Would it be reasonable to use plasma
in this case, or would it be a problem due to the fact that the
protein is so highly negative?

Lars Skjaerven
University of Bergen
Norway
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