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Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
被引:34
|作者:
Aviat, Felix
[1
]
Levitt, Antoine
[2
,3
]
Stamm, Benjamin
[4
,5
,6
]
Maday, Yvon
[7
,8
,9
]
Ren, Pengyu
[10
]
Ponder, Jay W.
[11
]
Lagardere, Louis
[1
,12
]
Piquemal, Jean-Philip
[1
,8
]
机构:
[1] UPMC Univ Paris 06, Lab Chim Theor, UMR 7617, F-75005 Paris, France
[2] Inria Paris, F-75589 Paris 12, France
[3] Univ Paris Est, CERMICS ENPC, F-77455 Marne La Vallee, France
[4] Rhein Westfal TH Aachen, Dept Math, MATHCCES, Schinkelstr 2, D-52062 Aachen, Germany
[5] Forschungszentrum Julich, Computat Biomed, Inst Adv Simulat IAS 5, D-52425 Julich, Germany
[6] Forschungszentrum Julich, Inst Neurosci & Med INM 9, D-52425 Julich, Germany
[7] UPMC Univ Paris 06, Lab Jacques Louis Lions, UMR 7598, F-75005 Paris, France
[8] Inst Univ France, F-75231 Paris 05, France
[9] Brown Univ, Div Appl Math, Providence, RI 02912 USA
[10] Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USA
[11] Washington Univ, Dept Chem, Campus Box 1134,One Brookings Dr, St Louis, MO 63130 USA
[12] UPMC Univ Paris 06, Inst Calcul & Simulat, F-75005 Paris, France
基金:
美国国家卫生研究院;
关键词:
PARTICLE MESH EWALD;
SCALABLE EVALUATION;
DYNAMICS;
FIELD;
COMPUTATIONS;
MECHANICS;
EQUATIONS;
PROTEINS;
WATER;
D O I:
10.1021/acs.jctc.6b00981
中图分类号:
O64 [物理化学(理论化学)、化学物理学];
学科分类号:
070304 ;
081704 ;
摘要:
We introduce a new class of methods, denoted as Truncated Conjugate Gradient(TCG), to solve the many-body polarization energy and its associated forces in molecular simulations (i.e. molecular dynamics (MD) and Monte Carlo). The method consists in a fixed number of Conjugate Gradient (CG) iterations. TCG approaches provide a scalable solution to the polarization problem at a user-chosen cost and a corresponding optimal accuracy. The optimality of the CG-method guarantees that the number of the required matrix-vector products are reduced to a minimum compared to other iterative methods. This family of methods is non-empirical, fully adaptive, and provides analytical gradients, avoiding therefore any energy drift in MD as compared to popular iterative solvers. Besides speed, one great advantage of this class of approximate methods is that their accuracy is systematically improvable. Indeed, as the CG-method is a Krylov subspace method, the associated error is monotonically reduced at each iteration. On top of that, two improvements can be proposed at virtually no cost: (i) the use of preconditioners can be employed, which leads to the Truncated Preconditioned Conjugate Gradient (TPCG); (ii) since the residual of the final step of the CG-method is available, one additional Picard fixed point iteration ("peek"), equivalent to one step of Jacobi Over Relaxation (JOR) with relaxation parameter omega, can be made at almost no cost. This method is denoted by TCG-n(omega). Black-box adaptive methods to find good choices of omega are provided and discussed. Results show that TPCG-3(omega) is converged to high accuracy (a few kcal/mol) for various types of systems including proteins and highly charged systems at the fixed cost of four matrix-vector products: three CG iterations plus the initial CG descent direction. Alternatively, T(P)CG-2(omega) provides robust results at a reduced cost (three matrix-vector products) and offers new perspectives for long polarizable MD as a production algorithm. The T(P)CG-1(omega) level provides less accurate solutions for inhomogeneous systems, but its applicability to well-conditioned problems such as water is remarkable, with only two matrix-vector product evaluations.
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页码:180 / 190
页数:11
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