[gmx-users] how to calculate the normal of plane for Tryptophan or how to get the comparison matrix in g_rms

I send this message yesterday, but I myself donot see this message, so, I send it again, very sorry for the spam. Dear gmxer's I am simulating a protein, want to calculate the normal of plane for Tryptophan residue amino acid in that protein. We need to take into account that, in simulation, atoms

[gmx-users] how to calculate the normal of plane for Tryptophan or how to get the comparison matrix in g_rms

Dear gmxer's I am simulating a protein, want to calculate the normal of plane for Tryptophan residue amino acid in that protein. We need to take into account that, in simulation, atoms of TRP vibrate all the time, and they are not always on the same plane: If they were on the same plane in my simul

Re: [gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?

s a plus, right? Any suggestions or comments are very welcome. Thank you. yours xiaodong Research School of Chemistry ANU On Tue, Jun 21, 2011 at 11:21 PM, Justin A. Lemkul wrote: > > > xiaodong huang wrote: > >> Dear gromacs-ers >> >> I am using stochastic dynamics integ

[gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?

or clues are very welcome. Yours xiaodong huang Research School of Chemistry ANU -- gmx-users mailing listgmx-users@gromacs.org 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&#