evaluation of fast electrostatics algorithms alice n. ko and jesús a. izaguirre with thierry...
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Evaluation of Fast Evaluation of Fast Electrostatics AlgorithmsElectrostatics Algorithms
Alice N. Ko and Jesús A. Izaguirre
with Thierry Matthey
Department of Computer Science and EngineeringUniversity of Notre Dame, USADepartment of InformaticsUniversity of Bergen, NORWAY
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Executive summaryExecutive summary
How to choose the best among Particle Mesh Ewald (PME), Multi-Grid (MG) summation, Ewald
sum, for molecular dynamics of biological molecules. Why should your next simulation
consider using MG?
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Problem: Full Electrostatic Problem: Full Electrostatic EnergyEnergy
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Motivation Motivation Fast evaluation of full electrostatics in molecular
dynamics (MD) of biological molecules important for accuracy in many applications
Structural stability of DNA and proteins Ionic environments
Many methods exist to do explicit evaluation of fast electrostatics
Fast Multipole Method O(N) Greengard, 1987 Particle Mesh Ewald O(N log N) Darden, 1993 Multi-grid summation O(N) Brandt, 1990
Skeel, 2002 Which one to use for a given system and
accuracy?
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ObjectivesObjectives
1. Provide practical guidelines for choosing parameters for each algorithm
2. Evaluate competitive algorithms
3. Evaluate suitability of MG to MD simulations
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Particle Mesh EwaldParticle Mesh Ewald Following Ewald, separates the
electrostatic interactions into two parts: Direct-space short range evaluation Fourier-space evaluation
The Fourier term is approximated by using fast Fourier transforms on a grid
Method parameters are grid size and cutoff of direct-space
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Multigrid IMultigrid I
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Multigrid IIMultigrid II
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Related Work IRelated Work I
Darden et al., J. Chem. Phys. 1993 effect of varying parameters of Particle Mesh Ewald
Petersen et al., J. Chem. Phys. 1995 accuracy and efficiency of Particle Mesh Ewald (PME)
Krasny et al., J. Chem. Phys. 2000 used FMM to compute direct part of Ewald sum
Skeel et al., J. Comp. Chem. 2002 study of parameters for multigrid (MG) method.
Compared MG to Fast Multipole Method (FMM). MG faster than FMM for low accuracy
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Related Work IIRelated Work II
Most published results fail to suggest how to determine the
specific values provide general trends only contain unknown constants in
equations that model performance
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SummarySummary General contributions of this study
Practical guidelines for choosing parameters for each algorithm, and to choose among different algorithms
Implemented important algorithms with reasonable efficiency in ProtoMol
Tested algorithms for various system sizes and accuracy
Tested quality of these methods for MD of solvated proteins
Encapsulated results of this study on a tool called MDSimAid
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Experimental protocolExperimental protocol These methods were tested and implemented:
1. Smooth Particle Mesh Ewald2. Multigrid summation3. Ewald summation
Testing protocol: Methods (1) and (2) above were compared against (3)
to determine accuracy and relative speedup Tested on water boxes and protein systems ranging
from 1,000 to 100,000 atoms, and low and high accuracies
CHARMM used to prepare systems, NAMD and ProtoMol used for simulations
Determined optimal parameters for each method for a given accuracy and system size
For selected protein systems, structural and transport properties were computed (e.g., Melittin, pdb id 2mlt, in water, 11845 atoms)
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Solvated MelittinSolvated Melittin
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ResultsResults Big picture
Multi-grid summation is an effective method for low accuracy computation of full electrostatics
For low accuracy, Multi-Grid is faster than PME and Ewald for all system sizes tested (from 1000 to 100,000)
For medium accuracy, Multi-Grid is faster than PME for systems of 8,000 atoms or more
Multi-grid with low accuracy produces correct structural and dynamic properties
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Results (10Results (10-4-4 rPE) rPE)
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Results (10Results (10-5-5 rPE) rPE)
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RDFRDF
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Multigrid IIIMultigrid III Complex relationship among method
parameters: Cutoff and softening distances for potential
evaluation at the particle and grid levels Grid size and interpolation order Number of levels
Rules extracted from extensive evaluation encapsulated in MDSimAid
Fine tuned at run-time by running selected tests
Makes method easier to use
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Simulation Results for Simulation Results for MelittinMelittin
PME requires about 3% of the CPU time (17 days 20 hours) when measured against Ewald
MG in pbc requires only about 1% MG is about 66% faster than PME
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DiscussionDiscussion MG is a competitive method for low accuracy MD
simulations Accuracy not a great concern for long time simulations MG would be natural choice for multiple time stepping
integrators To choose among methods, and good parameters for
each method, MDSimAid is a useful tool For further reference:
http://www.nd.edu/~lcls/mdsimaid http://www.nd.edu/~lcls/protomol http://www.ks.uiuc.edu/development/namd http://www.nd.edu/~izaguirr
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AcknowledgementsAcknowledgements
This research was supported by an NSF Biocomplexity grant and an NSF CAREER award