I think that what you're seeing is reasonable and expected.
with use_pme=0, you basically have a cutoff on long-range
electrostatics and thus there are large fluctuations as
atoms move in and out of the cutoff. this "one factor" is
a really important one...
----- Original Message -----
From: "Linda Prengaman" <lindap.cmu.edu>
To: <amber.scripps.edu>
Sent: Thursday, May 27, 2004 3:42 PM
Subject: AMBER: Amber 7 (sander) use of PME
> Hello,
> 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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Received on Thu May 27 2004 - 21:53:00 PDT
