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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| Vydáno v: | Computer physics communications Ročník 288; s. 108742 |
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| Hlavní autoři: | , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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Elsevier B.V
01.07.2023
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| ISSN: | 0010-4655, 1879-2944, 1879-2944 |
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| Abstract | 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. |
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| AbstractList | 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. 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. |
| ArticleNumber | 108742 |
| Author | Alastruey-Benedé, Jesús Sancho, Javier López-Villellas, Lorién García-Risueño, Pablo Marco-Sola, Santiago Ibáñez, Pablo Galano-Frutos, Juan José Kjelgaard Mikkelsen, Carl Christian Moretó, Miquel |
| Author_xml | – sequence: 1 givenname: Lorién surname: López-Villellas fullname: López-Villellas, Lorién organization: Barcelona Supercomputing Center, Barcelona, Spain – sequence: 2 givenname: Carl Christian surname: Kjelgaard Mikkelsen fullname: Kjelgaard Mikkelsen, Carl Christian organization: Department of Computing Science and HPC2N, Umeå, Sweden – sequence: 3 givenname: Juan José surname: Galano-Frutos fullname: Galano-Frutos, Juan José organization: Department of Biochemistry, Molecular and Cellular Biology / Biocomputation and Complex Systems Physics Institute (BIFI), Universidad de Zaragoza, Zaragoza, Spain – sequence: 4 givenname: Santiago surname: Marco-Sola fullname: Marco-Sola, Santiago organization: Barcelona Supercomputing Center, Barcelona, Spain – sequence: 5 givenname: Jesús orcidid: 0000-0003-4164-5078 surname: Alastruey-Benedé fullname: Alastruey-Benedé, Jesús email: jalastru@unizar.es organization: Departamento de Informática e Ingeniería de Sistemas / Aragón Institute for Engineering Research (I3A), Universidad de Zaragoza, Zaragoza, Spain – sequence: 6 givenname: Pablo surname: Ibáñez fullname: Ibáñez, Pablo organization: Departamento de Informática e Ingeniería de Sistemas / Aragón Institute for Engineering Research (I3A), Universidad de Zaragoza, Zaragoza, Spain – sequence: 7 givenname: Miquel surname: Moretó fullname: Moretó, Miquel organization: Barcelona Supercomputing Center, Barcelona, Spain – sequence: 8 givenname: Javier surname: Sancho fullname: Sancho, Javier organization: Department of Biochemistry, Molecular and Cellular Biology / Biocomputation and Complex Systems Physics Institute (BIFI), Universidad de Zaragoza, Zaragoza, Spain – sequence: 9 givenname: Pablo surname: García-Risueño fullname: García-Risueño, Pablo email: risueno@unizar.es |
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| CitedBy_id | crossref_primary_10_1080_21691401_2025_2531748 crossref_primary_10_1002_cpe_7853 crossref_primary_10_1002_slct_202405189 crossref_primary_10_1021_acs_jctc_5c01376 crossref_primary_10_3390_mi14081512 |
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| Keywords | LINCS Molecular dynamics Newton's method Non-linear equations Constraint algorithms SHAKE |
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| SubjectTerms | Constraint algorithms LINCS Molecular dynamics Newton's method Non-linear equations nonlinear equations SHAKE |
| Title | Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code |
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