标题: GMX和lammps中的控温问题 [打印本页] 作者Author: Lacrimosa 时间: 2019-9-25 23:18 标题: GMX和lammps中的控温问题 1.在使用lammps的时候发现nvt系综默认使用的是Nose-hover恒温算法,而若要使用V-rescale恒温算法,则有这样的提示：（这里fix是设定控温算法和模拟系综等参数的指令）
Unlike the fix nvt command which performs Nose/Hoover thermostatting AND time integration, this fix does NOT perform time integration. It only modifies velocities to effect thermostatting. Thus you must use a separate time integration fix, like fix nve to actually update the positions of atoms using the modified velocities. Likewise, this fix should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by fix nvt or fix langevin commands.,
2.当查阅GMX手册的时候，也在3.4.8 Temperature coupling一节开头看到这样的话：
While direct use of molecular dynamics gives rise to the NVE (constant number, constant volume,constant energy ensemble),most quantities that we wish to calculate are actually from a constant temperature (NVT) ensemble, also called the canonical ensemble.When using temperature and/or pressure coupling the total energy is no longer conserved. Instead there is a conserved energy quantity the formula of which will depend on the combination or temperature and pressure coupling algorithm used.
这是不是就可以认为lammps中使用nve系综加v-rescale耦合=nvt系综了呢？作者Author: agent99 时间: 2019-9-26 02:29
我觉得不能说“使用nve系综”吧，毕竟最基本的md算法天然就是nve，lammps里的"fix nve"命令感觉其实就是调用一下md integrator的意思，而“fix nvt”就是把n-h thermostat和fix nve里的integrator给整合到一起了，个人理解作者Author: Mikasa 时间: 2019-9-27 10:20
fix nvt, fix npt
These commands perform time integration on Nose-Hoover style non-Hamiltonian equations of motion which are designed to generate positions and velocities sampled from the canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This updates the position and velocity for atoms in the group each timestep.
Only the nvt fixes perform time integration, meaning they update the velocities and positions of particles due to forces and velocities respectively. The other thermostat fixes only adjust velocities; they do NOT perform time integration updates.
fix temp/berendsen
Unlike the fix nvt command which performs Nose/Hoover thermostatting AND time integration, this fix does NOT perform time integration. It only modifies velocities to effect thermostatting. Thus you must use a separate time integration fix, like fix nve to actually update the positions of atoms using the modified velocities. Likewise, this fix should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by fix nvt or fix langevin commands.
作者Author: YZH_jesse 时间: 2020-12-5 21:02
各位老师好
我在 “Blockage of Water Flow in Carbon Nanotubes by Ions Due to Interactions between Cations and Aromatic Rings” 这篇发表在PRL的文献上看到作者使用了 NVT 加 Langevin 热浴，耦合时间为 0.5 ps，但我在LAMMPS的手册上看到和楼主一样的问题，就Langevin热浴不对时间进行积分。