Re: [gmx-users] g_bar for larger systems (protein-protein interaction)

2013-02-26 Thread Ricardo Soares
On Mon, 25 Feb 2013 15:55:05 -0500, Michael Shirts wrote > My personal opinion is that for large protein-protein calculations, > the free energy should be computed through potential of mean force > calculations, NOT alchemical methods, using the endpoints (properly > corrected) to determine the fre

Re: [gmx-users] g_bar for larger systems (protein-protein interaction)

2013-02-25 Thread Michael Shirts
My personal opinion is that for large protein-protein calculations, the free energy should be computed through potential of mean force calculations, NOT alchemical methods, using the endpoints (properly corrected) to determine the free energy of association. There are a number of tutorials and exa

[gmx-users] g_bar for larger systems (protein-protein interaction)

2013-02-25 Thread Ricardo O. S. Soares
Hello dear users, I just took a look at the new gromacs paper at Bioinformatics, and I noticed a new tool g_bar, which is used for free energy calculations. I also found a nice tutorial by Justin Lemkul. While I'm adapting the workflow to my system, I'd like to know from anyone with more exper