Dear Yunpeng, Thanks for your instructions very much.
You mean I should use Nose MD. I doubt whether the Nose MD method can provide me a more non-local minimum? I want to get some configuration more steady than DFT gives. If I inspect as many non-local minimum as possible, I should try different initial configurations to run the MD. Is that so? Another question is I have no idea what the temperature of which should the system be under during the simulation. So how the option MD.InitialTemperature and MD.TargetTemperature should give. I looked up some examples, they can be different and need not to be the same temperature (so why we call Nose MD the constant temperature MD?) And can you explain me the role of MD.NoseMass? I have no idea just from the manual. Thank you in advance. Best wishes. Guangping 2011-10-02 Guangping Zhang 发件人: Yunpeng Wang <yunpengwan...@gmail.com> 发送时间: 2011-10-01 23:34 主 题: Re: [SIESTA-L] MD simulation in SIESTA 收件人: siesta-l@uam.es Firstly, number of atoms in your system is a constant, so your ensemble should contain a "N". Secondly, you want to simulate a surface with respect to a vacuum, so there must be no "P" in your ensemble. Thirdly, you want the molecule to adsorb on surface and during the process, energy will change, no "E". Otherwise, you can not get a steady solution. Finally, obviously, the answer is "NVT". Yun-Peng On Sat, Oct 1, 2011 at 7:39 PM, Guangping Zhang <zgp...@126.com> wrote: Dear siesta users: I want to do some molecular dynamics run using SIESTA to investigate the adsorbtion process of a molecule on a metal surface. I have looked into some materials for MD simulation using SIESTA. And leart that Verlet : is suit for NVE ensemble dynamics,where the number of particle and the Volume of the system and Total eneryg of the system are constant. Nose MD: NVT dynamics ParrinelloRahman:NPE dynamics with P-R barastat NoseParrinelloRahman MD:NPT dynamics with thermostat/barostat Anneal MD: Anneal to specified P and T. So different method is suit for different ensembles. I wonder whether the choose of different ensembles has obvious effect on the results? And which method is the best one for my system? Please give some instructions and comments. Thanks in advance. Best Guangping 2011-10-01 Guangping Zhang -- Yunpeng Peter Wang
