|> Hi, all: |> I was trying to use pcoupl= Parrinello-Rahman, pcouptype=anisotropic |> to do pressure coupling for anisotropic material (like crystal). It |> seems that I need six components for compressibility (xx yy zz xy yz |> xz). How do I get these six components before I do any MD simulation? | |Surely there are published results that you can refer to for these types of |considerations.
Well, anyone used anisotropic pressure coupling in gromacs can share a link of literature which contains those compressibility components they can use and used in gromacs? I have no idea how the all the components compressibility be calculated ( for my wurtzite crystal) and used in gromacs to conduct a anisotropic pressure coupling. Any shared experience will be appropriated. |> Also, if the compressibility changes with temperature and pressure, how |> can we use a fixed value of compressibility to simulate a system that |> changes from one state to another? Or the compressibility is not so |> sensitive to temperature and pressure? | |You can change temperature with simulated annealing, but how do you expect to |modulate the pressure? There's no way to systematically alter the pressure. If |your goal is to alter these factors somehow, then you have a very complicated |situation, and there is no really easy way to do it. You may have to do |different simulations under different conditions using known compressibilities. | |> Anyone has experience in using Parrinello-Rahman? Thanks in advance. | |Sure, many people do. What is it that you want to know about it? | |-Justin > Thanks, > Shuangxing Dai > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ========================================
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