[gmx-users] Normal Mode Analysis

James Starlight jmsstarlight at gmail.com
Fri Oct 14 20:58:59 CEST 2011

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 ?

Thank you for your help

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