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On 16/10/2011 4:31 AM, James Starlight wrote:
<blockquote
cite="mid:CAALQopwLdbNKEw_HRTaq873R2O4ddgd2APggvEHxCzJXS-iEZw@mail.gmail.com"
type="cite">Thanks<br>
It's works fine but I'venot find significant increasing in the
simulation speed :)<br>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAALQopwLdbNKEw_HRTaq873R2O4ddgd2APggvEHxCzJXS-iEZw@mail.gmail.com"
type="cite">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 )?<br>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopwLdbNKEw_HRTaq873R2O4ddgd2APggvEHxCzJXS-iEZw@mail.gmail.com"
type="cite">
<br>
<br>
James<br>
<br>
<div class="gmail_quote">2011/10/15 lina <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>
<div class="h5">On Sat, Oct 15, 2011 at 2:58 AM, James
Starlight <<a moz-do-not-send="true"
href="mailto:jmsstarlight@gmail.com">jmsstarlight@gmail.com</a>>
wrote:<br>
> Dear Gromacs users!<br>
><br>
> I have couple of questions about some Gromacs
features.<br>
><br>
><br>
> 1- I'm looking for tutorial where I could find clear
example of force fied<br>
> based Normal Mode Analysis via Gromacs<br>
><br>
> E.g on first step I would like to prepare structure
of my protein in<br>
> pereodic boundary conditions and conduct energy
minimization ( I've already<br>
> can do it). Next I'd like to conduct full-atomic
Normal Mode analysis and<br>
> obtain motion trajectories along some lowest
frequency modes for futher<br>
> visualization in VMD. Finally I'd like to obtain
information about<br>
> frequencies ( eigenvalues) of each mode as well as
frequencies of each<br>
> residue fluctuations along different modes.<br>
><br>
><br>
> 2- Also I'm looking for possible ways to enhanse
Gromacs efficiency eg via<br>
> ussage of multi cores of my CPU. I've found possible
sillution via MPI<br>
> function but this way dowsnt work in my case. How I
can activate<br>
> hyperthreading function as well as other possible
ways ?<br>
<br>
</div>
</div>
If you installed from src, during configure<br>
--enable-threads<br>
<br>
if you installed via some package management tools, I guess
they would<br>
install this way by default.<br>
<br>
try:<br>
<br>
mdrun -t<br>
<div class="im"><br>
><br>
><br>
> Thank you for your help<br>
><br>
> James<br>
><br>
</div>
> --<br>
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