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 James
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