[gmx-users] Normal Mode Analysis

[Mark Abraham]

On 16/10/2011 4:31 AM, James Starlight wrote:
> Thanks
> It's  works fine but I'venot find significant increasing in the 
> simulation speed :)

If you've configured with threads, then executing mdrun will spawn as 
many threads as you have physical cores. This will speed up the 
calculation so long as it runs for more than a few seconds.

> but I'd also to test MPI. Could you tell me what exactly ( MPI or 
> threading) might provide better productivity in case of big 
> heterogenious system ( e.g protein in membrane )?

It depends. MPI is required if your processors are not on the same piece 
of silicon, and is almost as good as threading if they are. Threading 
works if they are.

Mark

>
>
> James
>
> 2011/10/15 lina <lina.lastname at gmail.com <mailto:lina.lastname at gmail.com>>
>
>     On Sat, Oct 15, 2011 at 2:58 AM, James Starlight
>     <jmsstarlight at gmail.com <mailto:jmsstarlight at gmail.com>> wrote:
>     > Dear Gromacs users!
>     >
>     > I have couple of questions about some Gromacs features.
>     >
>     >
>     > 1- I'm looking for tutorial where I could find clear example of 
>     force fied
>     > based Normal Mode Analysis via Gromacs
>     >
>     > E.g on first step I would like to prepare structure of my protein in
>     > pereodic boundary conditions and conduct energy minimization (
>     I've already
>     > can do it). Next I'd like to conduct full-atomic Normal Mode
>     analysis and
>     > obtain motion trajectories along some lowest frequency modes for
>     futher
>     > visualization in VMD. Finally I'd like to obtain information about
>     > frequencies ( eigenvalues) of each mode as well as frequencies
>     of each
>     > residue fluctuations along different modes.
>     >
>     >
>     > 2- Also I'm looking for possible ways to enhanse Gromacs
>     efficiency eg via
>     > ussage of multi cores of my CPU. I've found possible sillution
>     via MPI
>     > function but this way dowsnt work in my case. How I can activate
>     > hyperthreading function as well as other possible ways ?
>
>     If you installed from src, during configure
>     --enable-threads
>
>     if you installed via some package management tools, I guess they would
>     install this way by default.
>
>     try:
>
>     mdrun -t
>
>     >
>     >
>     > Thank you for your help
>     >
>     > James
>     >
>     > --
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