On Sat, Oct 15, 2011 at 2:58 AM, James Starlight <[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 > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
