Forgive me if these questions are easily available somewhere but I have
not found them:
1. Timings:
Could anyone share timings for MD simulations using POL3 and AMOEBA
water boxes?
2. Does anyone have successful experience running POL3 or AMOEBA in
AMBER for 500ps to 5000ps which they could share with me?
3. General use questions:
How well are polarizable force fields working in AMBER?
Review of the archived mailing list shows two examples of researchers
having trouble with simple heating protocols or having issues
reproducing published results for FEP calculations. If someone were
wanting to reproduce the Meng 1994 (J. Am. Chem. SOC. 1994,116,
12061-12062) paper for acetate and methyl-ammonium solvation free energy
by FEP and then extend it, could they do so?
Regards
-- Den
--
any problem worth attack
proves its worth by fighting back
Piet Heins "Grooks"
D.G. Sprous, PhD
BioLeap Inc.
Cambridge MA 02141
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Received on Wed Aug 17 2011 - 08:30:02 PDT
