On the use of multiple‐time‐step algorithms to save computing effort in molecular dynamics simulations of proteins

Autor: Pechlaner, Maria, Oostenbrink, Chris, van Gunsteren, Wilfred F.
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Zdroj: Journal of Computational Chemistry
ISSN: 1096-987X
0192-8651
Popis: Computer simulation of proteins in aqueous solution at the atomic level of resolution is still limited in time span and system size due to limited computing power available and thus employs a variety of time‐saving techniques that trade some accuracy against computational effort. Examples of such time‐saving techniques are the application of constraints to particular degrees of freedom or the use of a multiple‐time‐step (MTS) algorithm distinguishing between particular forces when integrating Newton's equations of motion. The application of two types of MTS algorithms to bond‐stretching forces versus the remaining forces in molecular dynamics (MD) simulations of a protein in aqueous solution or of liquid water is investigated and the results in terms of total energy conservation and the influence on various other properties are compared to those of MD simulations of the same systems using bond‐length, and for water bond‐angle, constraints. At comparable computational effort, the use of bond‐length constraints in proteins leads to better energy conservation and less distorted properties than the two MTS algorithms investigated.
Computer simulation of proteins in aqueous solution is still limited by the required computing power. Here, we compare three time‐saving techniques: bond length constraints and two types of multiple‐time‐step (MTS) algorithms applying the high‐frequency bond‐stretching forces more frequently than the remaining ones. At comparable computational effort, the use of bond‐length constraints leads to better energy conservation and less distorted properties than the two MTS algorithms investigated.
Databáze: OpenAIRE
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