On the use of intra-molecular distance and angle constraints to lengthen the time step in molecular and stochastic dynamics simulations of proteins.

ABSTRACT: 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. An example of such a time-saving technique is the application of constraints to particular degrees of freedom when integrating Newton's or Langevin's equations of motion in molecular dynamics (MD) or stochastic dynamics (SD) simulations, respectively. The application of bond-length constraints is standard practice in protein simulations and allows for a lengthening of the time step by a factor of three. Applying recently proposed algorithms to constrain bond angles or dihedral angles, it is investigated, using the

SUBMITTER: Pechlaner M 

PROVIDER: S-EPMC9293444 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature