Thanks<br>It's works fine but I'venot find significant increasing in the simulation speed :)<br>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>
<br><br>James<br><br><div class="gmail_quote">2011/10/15 lina <span dir="ltr"><<a 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></div><div class="h5">On Sat, Oct 15, 2011 at 2:58 AM, James Starlight <<a 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>
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