Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code

In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of physical phenomena that we can afford to simulate. We examine the existing algorithms and...

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Vydané v:Computer physics communications Ročník 288; s. 108742
Hlavní autori: López-Villellas, Lorién, Kjelgaard Mikkelsen, Carl Christian, Galano-Frutos, Juan José, Marco-Sola, Santiago, Alastruey-Benedé, Jesús, Ibáñez, Pablo, Moretó, Miquel, Sancho, Javier, García-Risueño, Pablo
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: Elsevier B.V 01.07.2023
Predmet:
Constraint algorithms
LINCS
Molecular dynamics
Newton's method
Non-linear equations
nonlinear equations
SHAKE
LINCS
Molecular dynamics
Newton's method
Non-linear equations
Constraint algorithms
SHAKE
ISSN:0010-4655, 1879-2944, 1879-2944
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Shrnutí:In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of physical phenomena that we can afford to simulate. We examine the existing algorithms and software for solving nonlinear constraint equations in parallel and we explain why it is necessary to advance the state-of-the-art. We present ILVES-PC, a new algorithm for imposing bond constraints on proteins accurately and efficiently. It solves the same system of differential algebraic equations as the celebrated SHAKE algorithm, but ILVES-PC solves the nonlinear constraint equations using Newton's method rather than the nonlinear Gauss-Seidel method. Moreover, ILVES-PC solves the necessary linear systems using a specialized linear solver that exploits the structure of the protein. ILVES-PC can rapidly solve constraint equations as accurately as the hardware will allow. The run-time of ILVES-PC is proportional to the number of constraints. We have integrated ILVES-PC into GROMACS and simulated proteins of different sizes. Compared with SHAKE, we have achieved speedups of up to 4.9× in single-threaded executions and up to 76× in shared-memory multi-threaded executions. Moreover, ILVES-PC is more accurate than P-LINCS algorithm. Our work is a proof-of-concept of the utility of software designed specifically for the simulation of polymers. •Default configurations of MD packages may lead to non-converged, unphysical results.•ILVES-PC solves the constraint equations of SHAKE but using the fast Newton's method.•ILVES-PC is faster and more accurate than the state-of-the-art (SHAKE, P-LINCS).•Chemical structure of polymers allows efficient parallel simulations.
ISSN:0010-4655
1879-2944
1879-2944
DOI:10.1016/j.cpc.2023.108742