[gmx-users] Normal Mode Analysis

[lina]

On Sat, Oct 15, 2011 at 2:58 AM, James Starlight <jmsstarlight at 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
>
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