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 <[email protected] <mailto:[email protected]>>
On Sat, Oct 15, 2011 at 2:58 AM, James Starlight
<[email protected] <mailto:[email protected]>> 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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