scidac meeting, san francisco, june 27-30, 2005 scalable molecular dynamics t.p.straatsma laboratory...
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SciDAC Meeting, San Francisco, June 27-30, 2005
Scalable Molecular DynamicsScalable Molecular DynamicsScalable Molecular DynamicsScalable Molecular Dynamics
T.P.StraatsmaLaboratory Fellow and Associate Division Director
Computational Biology and BioinformaticsComputational Sciences and Mathematics Division
Pacific Northwest National Laboratory
2 SciDAC Meeting, San Francisco, June 27-30, 2005
NWChem Molecular Science SoftwareNWChem Molecular Science Software
ENERGY
GRADIENT
OPTIMIZE
DYNAMICS
THERMODYNAMICS
QMD
QM/MM
ET
QHOP
INPUT
PROPERTY
PREPARE
ANALYZE
ESP
VIB
Classical Force Field
DFT
SCF: RHF UHF ROHF
MP2: RHF UHF
MP3: RHF UHF
MP4: RHF UHF
RI-MP2
CCSD(T): RHF
CASSCF/GVB
MCSCF
MR-CI-PT
CI: Columbus Full Selected
Integral API
Geometry
Basis Sets
PEigS
pFFT
LAPACK
BLAS
MA
Global Arrays
ecce
ChemIO
NWCHEM
3 SciDAC Meeting, San Francisco, June 27-30, 2005
Domain DecompositionDomain DecompositionDomain DecompositionDomain Decomposition
Two-dimensional representationDistributed data
reduces memory use
Locality of interactionsreduces communication
Fluctuating number of atomsrequires atom redistribution
Inhomogeneous distributionrequires dynamic load balancing
local nodenon-local node domain within short rangenon-local node domain within long rangenon-local node domain outside interaction range
4 SciDAC Meeting, San Francisco, June 27-30, 2005
Force EvaluationForce EvaluationForce EvaluationForce Evaluation
1. Asynchronous ga_get of coordinates in box on neighboring node
2. Calculation forces with all local boxes within cutoff radius
3. Accumulate local forces
4. Asynchronous ga_acc to accumulate forces in box on neighboring node
All data transfer by means of one-sided, asynchronous communication
coordinates x
forces f
node i node j
F= -U(x)
12
34
5 SciDAC Meeting, San Francisco, June 27-30, 2005
Particle-mesh EwaldParticle-mesh EwaldParticle-mesh EwaldParticle-mesh Ewald
1. Charge grid construction
2. Block to slab decomposition
3. 3D-fast Fourier transform
4. Reciprocal space energy & forces
5. 3D-fast Fourier transform
6. Slab to block decomposition
7. Atomic forces
1
2
3
4
5
6
7
All nodes Node sub-set
6 SciDAC Meeting, San Francisco, June 27-30, 2005
FlowchartFlowchartFlowchartFlowchart
get coordinates
accumulate forces
pair lists
forces
PME charge grid
FFT & PME k-space
PME forces
redistribution
load balancing
record trajectory
properties
record properties
synchronous communication
asynchronous communication
processor-sub set communication
no processor communication
global wait for processor sub set
time step
7 SciDAC Meeting, San Francisco, June 27-30, 2005
Timing AnalysisTiming AnalysisTiming AnalysisTiming AnalysisHaloalkane dehalogenase, force evaluation timings
Synchronization PME forces
Non-local forces
Local forces
Reciprocal PME (fft, f-grid)
PME node subset synchronization PME charge grid construction
PME wait
8 SciDAC Meeting, San Francisco, June 27-30, 2005
Load BalancingLoad BalancingLoad BalancingLoad Balancing
LocalRedistribution
CollectiveResizing
9 SciDAC Meeting, San Francisco, June 27-30, 2005
Dynamic Load BalancingDynamic Load BalancingDynamic Load BalancingDynamic Load Balancing
Haloalkanedehalogenase: Time per Step
0.1
1
10
100
1 10 100
Number of Processors
Sca
lin
g
IBM-SP
HP
Haloalkanedehalogenase: Scaling
1
10
100
1 10 100
Number of Processors
Sca
lin
g
IBM-SP
HP
Linear
10 SciDAC Meeting, San Francisco, June 27-30, 2005
Challenges for the DOEChallenges for the DOEChallenges for the DOEChallenges for the DOE
Environmental Legacy at Hanford and other DOE sites• Bioremediation
Environmental and Health Impact of Energy Use• Carbon sequestration• Nitrogen fixation
Production of Energy• Biofuels• Hydrogen
11 SciDAC Meeting, San Francisco, June 27-30, 2005
Molecular Basis for Microbial Adhesion Molecular Basis for Microbial Adhesion and Geochemical Surface Reactionsand Geochemical Surface Reactions
Molecular Basis for Microbial Adhesion Molecular Basis for Microbial Adhesion and Geochemical Surface Reactionsand Geochemical Surface Reactions
Microbes in the subsurface mediate a number of environmental, geochemical processes:
Uptake of metal ions, including environmentally recalcitrant metals
Adhesion to mineral surfaces Reduction and mineralization of ions at the microbial surface
Pseudomonas aeruginosa: Cu, Fe, Au, La, Eu, U, Yb, Al, Ca, Na, KShewanella putrefaciens: Fe, S, MnShewanella alga: Fe, Cr, Co, Mn, UShewanella amazonensis: Fe, Mn, SShewanella oneidensis MR1External reduction involving OM
cytochromes
12 SciDAC Meeting, San Francisco, June 27-30, 2005
Project ObjectivesProject ObjectivesProject ObjectivesProject Objectives
Molecular level characterization of:Microbial adhesion to mineral surfacesMetal ion concentration in microbial membranes
Focus on Gram-negative bacterial Outer Membrane
Computational Approach:Molecular modeling and molecular dynamics simulationsQuantum mechanical description of key functional groupsThermodynamic Modeling
13 SciDAC Meeting, San Francisco, June 27-30, 2005
Gram Negative Cell WallsGram Negative Cell WallsGram Negative Cell WallsGram Negative Cell Walls
14 SciDAC Meeting, San Francisco, June 27-30, 2005
LPS ofLPS of Pseudomonas aeruginosa Pseudomonas aeruginosaLPS ofLPS of Pseudomonas aeruginosa Pseudomonas aeruginosa
NAG1 NAG2 PP
KDO1 KDO2
HEP1
HEP2
PP
P
CONH2
GALL-ALA
GLC*
GLC1
GLC2
GLC3
RHA
RHA
FUC
MAN
MAN
30-50
Lip
id A
Core
LP
SO
ch
ain 1. Design of the Rough LPS Molecular Model
2. Determination of Electrostatic Model
15 SciDAC Meeting, San Francisco, June 27-30, 2005
LPS Membrane ConstructionLPS Membrane ConstructionLPS Membrane ConstructionLPS Membrane Construction
Distribution of functional groups and water in the outer membrane of P. aeruginosa.These results are used for thermodynamic modeling of ion adsorption in microbial membranes.
16 SciDAC Meeting, San Francisco, June 27-30, 2005
Phosphate ClusteringPhosphate ClusteringPhosphate ClusteringPhosphate Clustering
Outer Core Inner Core
These results lend support to the interpretation of recent XAS experiments carried out by J. Bargar at SLAC indicating that uranyl ions take up by microbial membranes exists in clusters involving phosphates.
17 SciDAC Meeting, San Francisco, June 27-30, 2005
Membrane Electrostatic PotentialMembrane Electrostatic PotentialMembrane Electrostatic PotentialMembrane Electrostatic Potential
Average Potential Across Membrane
Calc.: 100 mVExp.: 80 mV
18 SciDAC Meeting, San Francisco, June 27-30, 2005
Atomic Charges from 2D SCF-HF ESP FitAtomic Charges from 2D SCF-HF ESP FitAtomic Charges from 2D SCF-HF ESP FitAtomic Charges from 2D SCF-HF ESP Fit
Slab: Periodic
Hartree Fock
Fragment: Point Charges
Blue: 25 e·kJ/molRed: -25 e·kJ/mol
19 SciDAC Meeting, San Francisco, June 27-30, 2005
Membrane-Mineral InteractionsMembrane-Mineral InteractionsMembrane-Mineral InteractionsMembrane-Mineral Interactions
123
4 5
20 SciDAC Meeting, San Francisco, June 27-30, 2005
P. AeruginosaP. Aeruginosa Outer Membrane Proteins Outer Membrane ProteinsP. AeruginosaP. Aeruginosa Outer Membrane Proteins Outer Membrane Proteins
E. coli membrane protein FecA (Pautsch and Schultz, 1998) and homology modeled P. aeruginosa membrane protein FecA (Straatsma, unpublished)
E. coli membrane protein TolC (Pautsch and Schultz, 1998) and homology modeled P. aeruginosa membrane protein OprM (Wong et al., 2001)
E. coli membrane protein OmpA (Pautsch and Schultz, 1998) and homology modeled P. aeruginosa membrane protein OprF (Brinkman et al., 2000)
21 SciDAC Meeting, San Francisco, June 27-30, 2005
P. aeruginosaP. aeruginosa OprF OprFP. aeruginosaP. aeruginosa OprF OprF
22 SciDAC Meeting, San Francisco, June 27-30, 2005
Electron transfer in bacterial respirationElectron transfer in bacterial respirationElectron transfer in bacterial respirationElectron transfer in bacterial respiration
• Under anaerobic conditions, Shewanella frigidimarina is able to use extra-cellular iron as the electron acceptor in its respiration. The electron transfer pathway involves a number of cytochromes which deliver electrons from the cytoplasmic membrane to the periplasmic membrane, where iron reduction occurs.
• The electron transfer (ET) between the membranes is carried out by the respiratory enzyme flavocytochrome c3
fumarate reductase (Fcc3), which
contains four bis(histidine) hemes.
23 SciDAC Meeting, San Francisco, June 27-30, 2005
Electron Transfer in FccElectron Transfer in Fcc33 and Ifc and Ifc33 Electron Transfer in FccElectron Transfer in Fcc33 and Ifc and Ifc33
Flavocytochrome c3 fumarate reductase of Shewanella frigidimarina
24 SciDAC Meeting, San Francisco, June 27-30, 2005
Marcus’ theory of electron transferMarcus’ theory of electron transferMarcus’ theory of electron transferMarcus’ theory of electron transfer
4
1
2 3
electronic coupling relaxation energy activation energy
dxz, dyz
dx2-
y2
Fe(II)1A1 Fe(III)2A2
Low-spin electron transfer
dx
y
dz2
25 SciDAC Meeting, San Francisco, June 27-30, 2005
B3LYP Characterization of a model hemeB3LYP Characterization of a model hemeB3LYP Characterization of a model hemeB3LYP Characterization of a model heme
Ehs/ls
Ehs/ls
Ehs/ls
AEAls AEAhs
DehsDels
Dels Dehs
Ehs/ls
r(Fe-N) Å
En
erg
y kcal/
mol
Fe(III)
Fe(II)
Heme-801 Heme-802
Heme-803 Heme-804
ET donor/acceptor orbital dπ
26 SciDAC Meeting, San Francisco, June 27-30, 2005
• Computational protein structure prediction • Protein-protein complexes: cell signaling• Protein-membrane and mineral-membrane complexes • Extension to microsecond simulation times• Statistically accurate thermodynamic properties• Comparative trajectory analysis
• Enzyme catalysis using hybrid QM/MM methods• Extension toward millisecond simulation times• Protein folding and unfolding• Membrane transport of simple ions and small molecules• Membrane fusion, vesicle formation
• Scalability on next generation MPP and hybrid architectures
Computational Structural Biology ChallengesComputational Structural Biology ChallengesComputational Structural Biology ChallengesComputational Structural Biology Challenges
27 SciDAC Meeting, San Francisco, June 27-30, 2005
AcknowledgementsAcknowledgementsAcknowledgementsAcknowledgementsDr. Roberto D. Lins, ETH Lausanne, CH
Dr. Robert M. Shroll, Spectral Sciences, Boston, MA
Dr. Wlodek K. Apostoluk, Wroclaw University, Poland
Dr. Andy R. Felmy, Chemical Sciences Division, PNNLDr. Kevin M. Rosso, Chemical Sciences Division, PNNL
Professor David A. Dixon, University of Alabama
Dr. Erich R. Vorpagel, EMSL
DOE Office of Advanced Scientific Computing ResearchDOE Office of Basic Energy Science, Geosciences Research ProgramDOE Office of Biological and Environmental Research
EMSL Molecular Sciences Computing FacilityComputational Grand Challenge Application Projects