CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs.

ABSTRACT: Implicit solvent models are widely used because they are advantageous to speed up simulations by drastically decreasing the number of solvent degrees of freedom, which allows one to achieve long simulation time scales for large system sizes. CHARMM-GUI, a web-based platform, has been developed to support the setup of complex multicomponent molecular systems and prepare input files. This study describes an Implicit Solvent Modeler (ISM) in CHARMM-GUI for various generalized Born (GB) implicit solvent simulations in different molecular dynamics programs such as AMBER, CHARMM, GENESIS, NAMD, OpenMM, and Tinker. The GB models available in ISM include GB-HCT, GB-OBC, GB-neck, GBMV, and GBSW with the CHARMM and Amber force fields for protein, DNA, RNA, glycan, and ligand systems. Using th

SUBMITTER: Wang KW 

PROVIDER: S-EPMC9551160 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature