I don't think this is a question about new free energy code -- I think this is asking about the fact if you can do a free energy calculation by specifying the A and B variables in the topology, instead of using the MDP coupl-moltype arguments. This is actually the way free energy calculations were managed before 4.0, and is still supported.
The answer is yes, though it requires some experience with what's going on -- and I don't have time to document it all quite right now, as it's described relatively thoroughly in the manual. The one difference is that the coupl-moltype keywords makes it easy to decouple molecules (turn off the intermolecular but not intramolecular energies) from their environment, which is very hard (and sometimes impossible) to do by changing A and B states. If you want to turn off all interactions, then you can do it very straightforwardly by changing the top files. Best, Michael On Thu, Oct 6, 2011 at 2:42 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Fabian Casteblanco wrote: >> >> Hello Justin, >> >> I have a question about your tutorial. If I want to mutate one small >> group of a molecule, I would have to not provide 'couple_lambda0' and >> 'couple_lambda1', correct? I would essentially have to follow sec >> 5.7.4 in the Gromacs manual and I have to actually provide all state A >> variable and all state B variables. Gromacs would calculate the new B >> state parameters for bond lengths, angles, etc, correct? Are there >> any other major differences to account for? >> > > I have never attempted FEP with the new free energy code. Try a simple test > system first and make sure it works as expected. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-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-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-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-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
