Re: AMBER: performance of periodic vs. non-periodic simulation

From: Oliver Hucke <>
Date: Wed, 12 May 2004 13:42:50 -0700

Thanks very much for this detailed and informative reply!

I already looked into the possibility to combine a spherical shell of
water molecules just covering my protein with a PB representation of the
"ouside" part. But this lead to almost as many water molecules as needed
for the truncated octahedron. According to the manual only this usage of
the PB model is supported at the moment.
It would really be great to be able to combine a small cap of water with
the PB model...

Thanks again,


Thomas E. Cheatham, III wrote:
>>I am have tried to speed up my simulations by switching from a periodic
>>system with PME to a non-periodic system with a cap of ~300 water
> ...
>>I first used a non bonded cutoff of 12A for the non-periodic system.
>>This lead to fluctuations of ~1000 to 2000 kcal/mol of the electrostatic
>>energy (corresponding to 10% of the total energy) preventing equilibration.
>>Using a cutoff larger than my system and switching off the update of the
>>non-bonded pairlist solved this problem - but now the simulations are
>>significantly slower than for the periodic system (details below).
> This is primarily why most of the AMBER developers focus on improving PME
> simulation rather than finite representations. The cutoff is really what
> is killing you in terms of performance since it leads to a large number of
> pair interactions. There is a big difference between 8/12/15 angstroms in
> terms of the number of pairs; basically a 12 A cutoff is roughly 2x the
> cost of a 8 A, and a 15 is > 3x more expensive. With PME, we typically
> use a fixed cutoff in the 8-10 angstrom range and then the reciprocal part
> of the calculation only adds an additional 50% (depending on the size of
> the charge grid and FFT performance). Whereas PME scales as roughly
> NlogN, you cap simulation scales more like N**2.
> If you could get stable cap simulations with an 8 angstrom cutoff, it may
> be ok, however as you see, even with a larger cutoff there is tremendous
> instability. This is likely due to the vacuum-water interface; earlier work
> by BR Brooks on such systems estimated that the effective pressure on the
> center of such a system (due to the interfacial order) was in the range of
> ~1000's of atmospheres ( dP ~ 15000/R where R is the radius in angstroms)
> [Theor. Chem. Acc. 99, 279-288 (1998)]. In addition (if the cap force
> constant is not high) water may drift away; if the force constant is high,
> this only exacerbates the pressure issues.
> What you ideally would like is a finite representation that properly
> treats the outside as a continuum; there are many approaches in the
> literature ranging from stochastic boundary conditions (CL Brooks, etc.),
> finite representations (B. Roux, etc), reactions fields (W. van Gunsteren,
> etc.), to Poisson-Boltzmann (R. Luo, etc.). Jorgensen's group published a
> paper trying to develop a boundary potential that could fix the artifacts
> [J Comp Chem 16, 951-972 (1995)]; this is shown to be an incredibly
> complex process. The better the cap representation, the greater the cost.
> In my experience, PME has simply proven more efficient than most other
> approaches. Furthermore, the reaction field approaches likely have
> problems in non-homogeneous environments (like lipid bilayers); a recent
> paper shows that although the reaction fields work better than truncation,
> PME appears to perform the best [J Chem Phys B 108, 4485-4494 (2004)].
> Furthermore, the periodicity artifacts, while present, do not seem to be
> overly large (on the order of kT for a water solvated system) [Hunenberger
> and co-workers; J Chem Phys B 108, 774-788 (2004)].
> If you want to stick with current versions of AMBER, it is likely best to
> run with PME or possibly future versions that may include PB. Otherwise,
> CHARMM can do stochastic boundaries and other finite representations.
> Good luck,
> --tom
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Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
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Received on Wed May 12 2004 - 21:53:00 PDT
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