Accelerating Rosetta with OpenMM. Peter Eastman. RosettaCon, August 5, 2010
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1 Accelerating Rosetta with OpenMM Peter Eastman RosettaCon, August 5, 2010
2 What is OpenMM? OpenMM is a library for molecular modeling on high performance architectures.
3 Performance ns/day OpenMM AMBER GPU AMBER CPU 3 Villin headpiece, 576 atoms, GBSA, 2 fs time step, no cutoff, run on one GPU core of a Tesla S1070 and one CPU core of a 2.5 GHz Xeon E5420 3
4 The OpenMM Vision Rosetta AMBER Gromacs Custom Codes... Nvidia GPU ATI GPU Multi-core CPU Cell Processor Cluster
5 The OpenMM Vision Rosetta AMBER Gromacs Custom Codes... OpenMM Nvidia GPU ATI GPU Multi-core CPU Cell Processor Cluster
6 Features Standard Forces Standard bonded terms (harmonic bonds, angles, etc.) Coulomb and Lennard Jones nonbonded forces Reaction field, Ewald, and PME for long range Coulomb forces GBSA implicit solvent 6
7 Features (continued) Integrators 7 Verlet (leapfrog) Langevin Brownian Temperature/Pressure Coupling Andersen thermostat Monte Carlo barostat Energy Minimization L-BFGS
8 Custom Forces Allow arbitrary algebraic expressions for forces Example: Morse Potential CustomBondForce* bonds = new CustomBondForce("D*(1-exp(a*(r0-r)))^2"); bonds->addperbondparameter("d"); bonds->addperbondparameter("a"); bonds->addperbondparameter("r0"); 8
9 Custom Forces (continued) Algebraic expressions are converted to OpenCL code and compiled Very little performance cost A powerful tool for research and prototyping Available custom forces Bond/angle/torsion bonded terms Nonbonded pairwise forces External forces Hydrogen bond forces Implicit solvent models 9
10 Rosetta Hbond Potential Hbond connects donor and acceptor groups E = E δ (δ)f θ (θ)f Ψ (Ψ) + D2 D1 \ θ δ Ψ A1 A2 F sr (δ)( E θ,sr (θ)f Ψ (Ψ) + E Ψ,sr (Ψ)F θ (θ))+ F lr (δ)( E θ,lr (θ)f Ψ (Ψ) + E Ψ,lr (Ψ)F θ (θ)) E δ (δ), E θ,sr (θ), E θ,lr (θ), E Ψ,sr (Ψ), E Ψ,lr (Ψ) are derived from structure data F θ (θ), F Ψ (Ψ), F sr (δ), F lr (δ) are piecewise linear fading functions 10
11 OpenMM Implementation string energy = "ed(d)*fadetheta*fadepsi+" "fadeshort*(ethetashort(ctheta)*fadepsi+epsishort(cpsi)*fadetheta)+" "fadelong*(ethetalong(ctheta)*fadepsi+epsilong(cpsi)*fadetheta);" "fadeshort=min(min(100*(d-0.14), 1-25*(d-0.19)), 1);" "fadelong=min(25*(d-0.19), 1-(1/0.07)*(d-0.23));" "fadetheta=min(20*ctheta, 1);" "fadepsi=min(20*cpsi, 1);" "d=distance(a1,d1); ctheta=-cos(angle(a1,d1,d2)); cpsi=-cos(angle(d1,a1,a2))"; CustomHbondForce* force = new CustomHbondForce(energy); force->addfunction("ed", createdistancetable(), 0.14, 0.3, true); force->addfunction("ethetashort", createshortrangethetatable(), 0, 1, true); force->addfunction("ethetalong", createlongrangethetatable(), 0, 1, true); force->addfunction("epsishort", createshortrangepsitable(), 0, 1, true); force->addfunction("epsilong", createlongrangepsitable(), 0, 1, true); 11
12 A Complication The energy also depends on the type of chemical groups interacting E δ (δ), E θ,sr (θ), E θ,lr (θ), E Ψ,sr (Ψ), E Ψ,lr (Ψ) all have multiple versions for different types of acceptors 12
13 The Solution Define a per-acceptor parameter to specify the type Append the different versions of each function Use the parameter to select the correct range Type 0 Type 1 Type 2 13
14 Implementation with Types string energy = "ed(d-0.14+type*0.26)*fadetheta*fadepsi*step(d-0.14)+" "fadeshort*(ethetashort(ctheta+type)*fadepsi*step(ctheta)+" "epsishort(cpsi+type)*fadetheta*step(cpsi))+" "fadelong*(ethetalong(ctheta+type)*fadepsi*step(ctheta)+" "epsilong(cpsi+type)*fadetheta*step(cpsi));" "fadeshort=min(min(100*(d-0.14), 1-25*(d-0.19)), 1);" "fadelong=min(25*(d-0.19), 1-(1/0.07)*(d-0.23));" "fadetheta=min(20*ctheta, 1);" "fadepsi=min(20*cpsi, 1);" "d=distance(a1,d1); ctheta=-cos(angle(a1,d1,d2)); cpsi=-cos(angle(d1,a1,a2))"; 14
15 Acknowledgements Vijay Pande Rhiju Das Kyle Beauchamp NIH 15
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