enhanced sampling methods recovering <a> Accelerated MD Introduction to Accelerated Molecular Dynamics an enhanced sampling method
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1 enhanced sampling methods Introduction to Accelerated Molecular Dynamics an enhanced sampling method Yi Wang McCammon group Aug 2011, NBCR Summer Institute Umbrella sampling B. ROUX, "The calculation of the potential of mean force using computer simulations", Comp. Phys. Comm. 91, 1-8, Conformational flooding O. F. Lange, L. V. Schäfer, and H. Grubmüller. Flooding in GROMACS: Accelerated Barrier Crossings in Molecular Dynamics. J. Comput. Chem. 27: (2006) Adaptive biasing force Implementation in NAMD: Research/namd/2.6/ug/node35.html Metadynamics Laio, A.; Parrinello, M. (2002). "Escaping free-energy minima". Proceedings of the National Academy of Sciences of the United States of America 99 (20): and more.. non-boltzmann sampling reweighting Boltzmann distribution Accelerated MD recovering <a> non-boltzmann sampling Boltzmann distribution Donald Hamelberg, John Mongan and J. Andrew McCammon, J. Chem. Phys., 120: (2004).
2 amd modes Boosting the total potential algorithm The algorithm of amd Boosting the dihedral potential only Dual boost: protein->dihedral, rest->total Donald Hamelberg, John Mongan and J. Andrew McCammon, J. Chem. Phys., 120: (2004). Implementing amd in namd Parallelization Strategy Space decomposition Force decomposition Basic Components Patches Compute Objects A typical MD step under the hood The velocity verlet algorithm James C. Phillips, et. al., JCC, 26: (2005). time
3 implementation of amd A typical MD step --- on each patch implementation of amd Total-potential amd A new reduction class Run Compute Objects Report Energy for amd Report/Receive Energy time Y Wang, C.B. Harrison, K. Schulten, J.A. McCammon, 2011 Comput. Sci. Disc Dihedral-only amd Store dihedral force in a new amd force array The amd force array is only initiated and used when amddihe is on. Y Wang, C.B. Harrison, K. Schulten, J.A. McCammon, 2011 Comput. Sci. Disc running amd in namd Benchmark & Output Input parameters ( accelmd Is accelerated molecular dynamics active? Acceptable Values: on or off Default Value: off Description: Specifies if accelerated MD is active. accelmddihe Apply boost to dihedrals? Acceptable Values: on or off Default Value: on Description: Only applies boost to the dihedral potential. By default, accelmddihe is turned on and the boost energy is applied to the dihedral potential of the simulated system. WhenaccelMDdihe is turned off, amd switches to the accelmdt mode, and the boost is applied to the total potential. accelmde Threshold energy Acceptable Values: Real number Description: Specifies the threshold energy in the amd equations. accelmdalpha Acceleration factor Acceptable Values: Positive real number Description: Specifies the acceleration factor in the amd equations. accelmddual Use dual boost mode? Acceptable Values: on or off Default Value: off Description: When accelmddual is on, amd switches to the dual boost mode. Two independent boost potentials will be applied: one to the dihedral potential that is controlled by the parameters accelmde and accelmdalpha, and a second to the (Total - Dihedral) potential that is controlled by the accelmdte and accelmdtalpha parameters described below. amdd: 7% amdt: 12% TCL: Running for steps ACCELERATED MD: STEP 0 dv dvavg BOND ANGL DIHE IMPR ELEC VDW POT PRESSURE: GPRESSURE: ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
4 Choice of parameters an example Two free parameters: E and! Larger E and smaller! lead to higher acceleration levels. As! increases, V*(r) asymptotically approaches V(r).! cannot be zero. E = <V> + N * 0.2! = 1/5* (E - <V>) Alanine dipeptide alanine dipeptide choice of parameters Empirical equation: E = <V> + N * (0.2 to 0.5)! = 1/5* (E - <V>) Classic MD (cmd) (-159, 165) Accelerated MD (amd) (-159, 165) (78, -56) The optimal choice of E/! is systemspecific and may require trial-and-error runs for each system.
5 effect of amd parameters pros & cons Advantages Only two free parameters. amd requires no prior knowledge of the system, i.e., no reaction coordinate needs to be defined a priori. Limitations The exponential form used in reweighting can produce large statistical noise. smaller! Parameter scan can be expensive for large systems. bigger E development of amd More to read Donald Hamelberg, John Mongan and J. Andrew McCammon, JCP, 120: , Replica-exchange amd Mikolai Fajer, Donald Hamelberg and J. Andrew McCammon. JCTC, 4: , Selective boost Donald Hamelberg, César Augusto F. de Oliveira and J. Andrew McCammon, JCP, 127:155102, Mikolai Fajer, Donald Hamelberg and J. Andrew McCammon, JCTC, 4: , Markwick, P., C. Cervantes, B. Abel, E. Komives, M. Blackledge, J.A. McCammon. JACS., 132 (4), , Y Wang, C.B. Harrison, K. Schulten, J.A. McCammon, 2011 Comput. Sci. Disc J. Wereszczynski and J. Andrew McCammon. JCTC, 6: , Adaptive amd Phineus R. L. Markwick, Levi C. T. Pierce, David B. Goodin, J. Andrew McCammon, JPCL, 2: , 2011.
6 acknowledgement San Diego: the McCammon group prof. Andy McCammon Phineus Markwick Cesar de Oliveira Urbana-Champaign: the TCBG group Chris Harrison Jim Phillips Peter Freddolino
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