[gmx-users] Normal Mode Analysis
jmsstarlight at gmail.com
Sat Oct 15 19:31:47 CEST 2011
It's works fine but I'venot find significant increasing in the simulation
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 )?
2011/10/15 lina <lina.lastname at gmail.com>
> On Sat, Oct 15, 2011 at 2:58 AM, James Starlight <jmsstarlight at gmail.com>
> > 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
> > 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
> > 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
> > 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
> if you installed via some package management tools, I guess they would
> install this way by default.
> mdrun -t
> > Thank you for your help
> > James
> > --
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