AMBER Archive (2004)

Subject: AMBER: Amber 7 (sander) use of PME

From: Linda Prengaman (
Date: Thu May 27 2004 - 14:42:13 CDT

    I am running a system consisting of one amino acid solvated in a small
water box (~300 TIP3 waters), cut=8.0, box size is~ 20x20x20. I have
found that running MD simulations with use_pme=1 and use_pme=0 give me
very different results for the total system energy: if pme is turned
on, my total system energy is very nice and stable in a minimum energy
state, but if pme is turned off, this energy appears to fluctuate
wildly. I have been told that turning pme on is the "way to go"
because it's more accurate, but I'm concerned about the accuracy of my
simulation because of the differences between my results that come
from changing just this one factor. Can anyone please give me some
advice or explaination about using PME so I can resolve this? Thanks!

Linda Prengaman
Dept. of Chemistry
Carnegie Mellon University
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