Jian Liu Group @PKU
Theoretical Chemistry / Chemical Dynamics
We have implemented the efficient "middle" thermostat scheme into the lastest version of AmberTools (AmberTools19). It can be obtained by following the instructions on the official website. For the users who can only use AmberTools18, the updated files for the "middle" scheme for AmberTools18 can be downloaded from the GitHub webpage.
The tutorial for the "middle" scheme is available on the webpage. One is also encouraged to read the AMBER manual for more details. The "middle" thermostat scheme has been implemented for MD for classical statistics as well as primitive PIMD for quantum statistics. It can be used together with QM/MM and enhanced sampling techniques (such as replica exchange) in AMBER. One can do ab initio PIMD or MD for the canonical ensemble by using AMBER combined with other quantum chemistry packages.
Related papers:
Zhaoxi Sun, Payam Kalhor, Yang Xu, Jian Liu*,"Extensive Numerical Tests of the Leapfrog Integrator in the Middle Thermostat Scheme in Molecular Simulations", Chinese Journal of Chemical Physics, 34, 6, 932-948 (2021) [Invited contribution to the John Zhang Festschrift] https://doi.org/10.1063/1674-0068/cjcp2111242
Zhijun Zhang, Xinzijian Liu, Kangyu Yan, Mark Tuckerman, Jian Liu*, "A unified efficient thermostat scheme for the canonical ensemble with holonomic or isokinetic constraints via molecular dynamics", Journal of Physical Chemistry A, 123, 28, 6056-6079 (2019). (Invited contribution to "Young Scientist Virtual Special Issue") [https://doi.org/10.1021/acs.jpca.9b02771][pdf version] (Highlighted in JPC Virtual Issue on New Tools and Methods )
Xinzijian Liu, Jian Liu*, "Path integral molecular dynamics for exact quantum statistics of multi-electronic-state systems", Journal of Chemical Physics, 148, 102319 (2018) [https://doi.org/10.1063/1.5005059 Invited article for the JCP special topic issue on "Nuclear Quantum Effects"] [arXiv preprint] [pdf version]
Zhijun Zhang, Kangyu Yan, Xinzijian Liu, Jian Liu*, "A leap-frog algorithm-based efficient unified thermostat scheme via molecular dynamics", Chinese Science Bulletin，63(33), 3467-3483(2018) [Invited Contribution] [http://engine.scichina.com/doi/10.1360/N972018-00908 ] [pdf version]
Dezhang Li, Zifei Chen, Zhijun Zhang, Jian Liu*, "Understanding molecular dynamics with stochastic processes via real or virtual dynamics", Chinese Journal of Chemical Physics, 30, 735 (2017) [http://dx.doi.org/10.1063/1674-0068/30/cjcp1711223 Invited article for the CJCP special topic issue on "Chemical Dynamics"] pdf version from the CJCP website [arXiv preprint] [pdf version]
Zhijun Zhang, Xinzijian Liu, Zifei Chen, Haifeng Zheng, Kangyu Yan, Jian Liu*, "A unified thermostat scheme for efficient configurational sampling for classical/quantum canonical ensembles via molecular dynamics", Journal of Chemical Physics, 147, 034109 (2017) [http://dx.doi.org/10.1063/1.4991621] Supplementary material [arXiv preprint] [pdf version]
Jian Liu*, Dezhang Li, Xinzijian Liu, "A simple and accurate algorithm for path integral molecular dynamics", Journal of Chemical Physics, 145, 024103 (2016) [http://dx.doi.org/10.1063/1.4954990] Supplementary material [arXiv preprint (Paper + Supplemental materical)][pdf version]
Jian Liu*, Zhijun Zhang, "Path integral Liouville dynamics: Applications to infrared spectra of OH, water, ammonia, and methane", Journal of Chemical Physics, 144, 034307 (2016) [http://dx.doi.org/10.1063/1.4939953] [pdf version]