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

• Published in: Proteins, structure, function, and bioinformatics Vol. 90; no. 2; pp. 543 - 559
• Main Authors: Pechlaner, Maria, Gunsteren, Wilfred F.
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.02.2022; Wiley Subscription Services, Inc
• Subjects: Algorithms; Angles (geometry); Aqueous solutions; Chemical bonds; classical equations of motion; Computer applications; Computer simulation; Constraining; Constraint modelling; constraints; Equations of motion; Hydrogen atoms; Molecular dynamics; Molecular Dynamics Simulation; Protein Conformation; Proteins; Proteins - chemistry; Side effects; stochastic dynamics; Stochasticity; Trypsin; trypsin inhibitor; Trypsin inhibitors; trypsin inhibitor; molecular dynamics; constraints; classical equations of motion; stochastic dynamics
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.26251

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 protein trypsin inhibitor as test molecule, whether bond angles and dihedral angles involving hydrogen atoms or even stiff proper (torsional) dihedral angles as well as improper ones (maintaining particular tetrahedral or planar geometries) may be constrained without generating too many artificial side effects. Constraining the relative positions of the hydrogen atoms in the protein allows for a lengthening of the time step by a factor of two. Additionally constraining the improper dihedral angles and the stiff proper (torsional) dihedral angles in the protein does not allow for an increase of the MD or SD time step.