Thanks It's works fine but I'venot find significant increasing in the simulation speed :) 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 )?
James 2011/10/15 lina <lina.lastn...@gmail.com> > On Sat, Oct 15, 2011 at 2:58 AM, James Starlight <jmsstarli...@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 > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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