Some studies on generalized coordinate sets for polyatomic molecules

Li, Wenjin; Ma, Ao

doi:10.1063/1.4936773

Cited by 8 publications

(9 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…45 In the computation of energy flow quantities, exact separation between internal and external DOFs was achieved by proper choice of external coordinates, as detailed in a recent publication. 46…”

Section: A Methodsmentioning

confidence: 99%

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

2016

The Journal of Chemical Physics

Self Cite

103

View full text Add to dashboard Cite

Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.

show abstract

Section: A Methodsmentioning

confidence: 99%

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

2016

The Journal of Chemical Physics

Self Cite

103

View full text Add to dashboard Cite

show abstract

“…As shown in a recent paper, 48 this coordinate set can separate the six external movements from the internal ones. The internal coordinates consist of the bonds, angles, and dihedral angles (the BAT coordinates).…”

Section: B Decomposition Of the Potential Energymentioning

confidence: 99%

“…Therefore, the coordinate set we chose according to Ref. 48 is of minimum dependence between the potential energy on each coordinate and should be the preferred choice. More detailed explanations are presented in the supplementary material.…”

Section: B a Committor-free Procedures For Identifying Relevant Coordmentioning

confidence: 99%

“…As described in Ref. 48, a particular BAT coordinate can be chosen such that the forces on many of such coordinates are independent of the choice of the base of a BKS-tree, 49 from which the set of BAT coordinates are constructed. Thus the decomposition of potential energy in this coordinates set has the least dependence on the choice of the BKS-tree base.…”

Section: B Decomposition Of the Potential Energymentioning

confidence: 99%

See 1 more Smart Citation

A benchmark for reaction coordinates in the transition path ensemble

2016

The Journal of Chemical Physics

Self Cite

View full text Add to dashboard Cite

The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems. C 2016 AIP Publishing LLC. [http://dx

show abstract

“…It was reported that a complete set of coordinates can be constructed to separate the translational, rotational, and vibrational movements of the system . Thus, the translational, rotational, and vibrational components of EAWs can be obtained by the summation of EAWs on the corresponding coordinates.…”

Section: Methodsmentioning

confidence: 99%

Residue–Residue Mutual Work Analysis of Retinal–Opsin Interaction in Rhodopsin: Implications for Protein–Ligand Binding

2020

J. Chem. Theory Comput.

Self Cite

View full text Add to dashboard Cite

crystal structure of Batho (chain A of PDB ID 2G87). 1 ASP83 and GLU122 were considered to be neutral 2 while all other charged amino acids were set to default protonation states. The spatial positions of Batho with respect to the lipid bilayer were taken from the Orientations of Proteins in Membranes (OPM) database. 3 All histidines were protonated either in the N position (HIS65, HIS152, HIS195, and HIS278) or in the N δ position (HIS100 and HIS211) 4 . The Schiff base linkage between the retinal and LYS296 was positively charged. The retinal and all crystallographic water molecules were preserved, other heteroatoms were removed.The CHARMM-GUI web-server 5 was used to embed the Batho system in an explicit membrane bilayer, and then immerse the resulted protein-lipid system in a box of explicit waters and ions at physiological concentration. Two palmitoyl chains bound to CYS322 and CYS323 were added to Batho before it was inserted in the membrane, which consisted of 128 palmitoyl-oleoyl-phosphatidyl choline (POPC) lipids. The final system was neutral and the size of the periodic box was approximately 71×71×92Å 3 with 8589 water molecules, 20 sodium ions, and 18 chloride ions (see Fig. S6).Simulation Details All simulations were performed with the software suite GROMACS-5.1.1. 6The c36 CHARMM force field 7 was used for protein and lipids. The force field parameters of retinal were adapted from recent literatures. 8,9 The TIP3P water model was used. The energy of the system was first minimized with very strong position restraints to heavy atoms of the protein (including retinal and two palmitoyl chains bound to rhodopsin). The position of the phosphorus atom and two dihedrals of lipids were also restrained strongly. Then, the system was under a series of equilibration with position and dihedral restraints were gradually released. The early stage of equilibration was performed in the NVE ensemble, then all the subsequent simulations were switched to the NPT ensemble. The system was coupled to a Berendsen thermostat with τ t =1.0 ps to keep the temperature constant at 303.15 K, and a semiisotropic Berendsen barostat with τ p =5.0 ps to keep the pressure constant at 1 bar. 10 An integration time step of 2 fs was used with constraints to bonds involving hydrogen atoms using the LINCS algorithm. 11 Lennard-Jones interactions were calculated using S2

show abstract

Some studies on generalized coordinate sets for polyatomic molecules

Cited by 8 publications

References 30 publications

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

A benchmark for reaction coordinates in the transition path ensemble

Residue–Residue Mutual Work Analysis of Retinal–Opsin Interaction in Rhodopsin: Implications for Protein–Ligand Binding

Contact Info

Product

Resources

About