[gmx-users] Re: anisotropic pressure coupling

[Shuangxing Dai]

|> 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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