• Review •
Cheng Peng, Leyun Wu, Zhijian Xu, Weiliang Zhu. Replica Exchange Molecular Dynamics[J]. Progress in Chemistry, 2022, 34(2): 384-396.
Methods | CVs* | System | ref |
---|---|---|---|
RSE-MTD | dihedral angles, atomic distance, T | organic, peptide | |
w-REXAMD | dihedral boost parameters | organic, peptide | |
REUS/REST | Distance, potential energy(T) | protein-ligand | |
H-REMD/T-REMD | Restraint strength, T | RNA | |
ABMD+ REMD | Rg, T | organic | |
FEP/REST | λ,T | Protein-ligand | |
Tq-REM | q, T | peptide, protein | |
ossPTMetaD | NMA,T | protein-ligand, protein | |
Multidimensional REMD | pH, Ev, T | peptide |
Methods to improve the sampling efficiency of REMD | Examples | |
---|---|---|
1.Improve the approach and swapping rate of replica exchange | RPM, RSPM, Calvo’s all-pairs exchange, REMD-MSSA,infinite swapping REMD, DEWREM | |
2.Reduce the potential energy on exchange attempts | 1)Deal with the explicit solvent | hybrid REMD, kernel REMD, REMshH, vsREMD, hREMD |
2)Reduce the freedom of solute | PREMD, LREMD | |
3.Hamiltonians replica exchange molecular dynamics | 1)Adjust the formula of potential energy | H-REMD, vWREM, CREM, REX-TAMD, Q-REMD, REST1, REST2, REFT, gREST, FREM, MFREM, ResEx |
2)Adopted into other enhanced sampling algorithms | BE-MTD, essential dynamics, rex-GaMD, AMD, GaREUS, EDS, BP-REXMSλD | |
3)Multidimensional replica exchange molecular dynamics | RSE-MTD, w-REXAMD, REUS/REST, 2D REMD, ossPTMetaD, FEP/REST, ABMD-REMD, Tq-REM, Multidimensional REMD | |
4)Introducing physical parameters in simulations | V-REMD, surface-tension REMD, MSREMD, VTREMD | |
4.Adjust simulation process | 1)Change the way of temperature control | TIGER1, TIGER2, TIGER2h, TIGER2A, TIGER2hs, TIGER3, EE-REMD, CM-REMD, STMD, Modified REMD 1, Modified REMD 2 |
2)Adjust parameters in parallel replicas | Reservoir REMD, REDS, Convective REMD | |
3)Multilayer simulation in parallel replicas | MuSTAR MD, Multiplexed REMD, mQ-REMD | |
4)Adjust initial structures | NUMD+REMD, Onsager-Machlup/REMD | |
5.Change the sampling methods | Tsallis-REMD, RXSGLD, QM/MM-REMD, BOMD, SE-BOREMD, CPMD, ICMD, MCMD | |
6.Heterogeneous and distributed computing environment | gREMD, HaRE, ASyncRE |
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