[gmx-users] reaction field

Hello I would like to perform a molecular simulation with the AMBER99SB FF , tip3p water model and reaction field for long range interactions. Which value of epsilon_rf (The relative dielectric constant of the reaction field) do I have to use? Thanks Williams -- gmx-users mailing listgmx-us

[gmx-users] Re: Williams

Hello! What`s the meaning of the error "hi (0.00) <= lo (0.00)" that outputs g_cluster? Which the purpose of the option -rmsmin of g_cluster? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://

[gmx-users] Re: mass-weighted analysis

Hello GROMACS users I am Williams, the biochemistry student. If I want to calculate QH entropy and my fit and analysis group are the same, the covariance matrix must be mass weighted? Its a little bit confussing that part of the GROMACS manual Thanks -- gmx-users mailing listgmx-users@gromacs

[gmx-users] Re: Williams

Thanks for your advices. The fact is that even when the input of the eigenvalues is optional in g_anaeig, they must be provided besides the eigenvectors in order to obtain the same result as with the perl script. Williams -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] submision

-- 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't post (un)subscribe requests to the list. Use the www interface or send it to gmx-

[gmx-users] Re: quasi-harmonic entropy calculation

My name is Williams. I am a Biochemistry student. I have done QH entropy calculation using g_anaeig, but I found an old perl script at GROMACS web site to do the same. The problem is that when I calculate entropy for the loops of my protein the results are the same using g_anaeig or the old perl sc