TY - JOUR
T1 - CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods
AU - Suh, Donghyuk
AU - Feng, Shasha
AU - Lee, Hwayoung
AU - Zhang, Han
AU - Park, Sang Jun
AU - Kim, Seonghan
AU - Lee, Jumin
AU - Choi, Sun
AU - Im, Wonpil
N1 - Publisher Copyright:
© 2022 The Protein Society.
PY - 2022/11
Y1 - 2022/11
N2 - Enhanced sampling methodologies modifying underlying Hamiltonians can be used for the systems with a rugged potential energy surface that makes it hard to observe convergence using conventional unbiased molecular dynamics (MD) simulations. We present CHARMM-GUI Enhanced Sampler, a web-based tool to prepare various enhanced sampling simulations inputs with user-selected collective variables (CVs). Enhanced Sampler provides inputs for the following nine methods: accelerated MD, Gaussian accelerated MD, conformational flooding, metadynamics, adaptive biasing force, steered MD, temperature replica exchange MD, replica exchange solute tempering 2, and replica exchange umbrella sampling for the method-implemented MD packages including AMBER, CHARMM, GENESIS, GROMACS, NAMD, and OpenMM. Users only need to select a group of atoms via intuitive web-implementation in order to define commonly used nine CVs of interest: center of mass based distance, angle, dihedral, root-mean-square-distance, radius of gyration, distance projected on axis, two types of angles projected on axis, and coordination numbers. The enhanced sampling methods are tested with several biological systems to illustrate their efficiency over conventional MD. Enhanced Sampler with carefully optimized system-dependent parameters will help users to get meaningful results from their enhanced sampling simulations.
AB - Enhanced sampling methodologies modifying underlying Hamiltonians can be used for the systems with a rugged potential energy surface that makes it hard to observe convergence using conventional unbiased molecular dynamics (MD) simulations. We present CHARMM-GUI Enhanced Sampler, a web-based tool to prepare various enhanced sampling simulations inputs with user-selected collective variables (CVs). Enhanced Sampler provides inputs for the following nine methods: accelerated MD, Gaussian accelerated MD, conformational flooding, metadynamics, adaptive biasing force, steered MD, temperature replica exchange MD, replica exchange solute tempering 2, and replica exchange umbrella sampling for the method-implemented MD packages including AMBER, CHARMM, GENESIS, GROMACS, NAMD, and OpenMM. Users only need to select a group of atoms via intuitive web-implementation in order to define commonly used nine CVs of interest: center of mass based distance, angle, dihedral, root-mean-square-distance, radius of gyration, distance projected on axis, two types of angles projected on axis, and coordination numbers. The enhanced sampling methods are tested with several biological systems to illustrate their efficiency over conventional MD. Enhanced Sampler with carefully optimized system-dependent parameters will help users to get meaningful results from their enhanced sampling simulations.
KW - collective variables
KW - enhanced sampling
KW - molecular dynamics
KW - rare events
UR - http://www.scopus.com/inward/record.url?scp=85141004296&partnerID=8YFLogxK
U2 - 10.1002/pro.4446
DO - 10.1002/pro.4446
M3 - Article
C2 - 36124940
AN - SCOPUS:85141004296
SN - 0961-8368
VL - 31
JO - Protein Science
JF - Protein Science
IS - 11
M1 - e4446
ER -