Hi, I'd recommend alchemistry.org as a good place to start. Justin's tutorial (the one you linked to) is an example of an equilibrium free energy method, not a slow growth method. As a general rule, equilibrium methods are easier to use and are recommended for people without extensive experience.
The following paper did something similar to what you're looking to do: https://www.google.be/url?sa=t&source=web&rct=j&url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872215/&ved=0ahUKEwjq3I7M-YbMAhXI_w4KHQeeCX8QFggoMAU&usg=AFQjCNHnkqQys4V7UYCURTPZyKQEYrGdWQ&sig2=rpmfKD8E07TCQ_XfeUyE3Q It might be worth looking into their methodology. Good luck Dries On 11 Apr 2016 5:41 p.m., "Tushar Ranjan Moharana" < tusharranjanmohar...@gmail.com> wrote: Hi everyone, I want to calculate difference in folding free energy due to certain mutations. I want to follow the slow growth method as mentioned in: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/02_topology.html However I don't know how to prepare dual topology (even after reading manual, section 5.7.4). I want to use gromos 53a6 force field. Can anyone tell me how to prepare dual topology. Any link to read or tutorial will be of great help. Thanks a lot for the help. "A society with free knowledge is better than a society with free food" Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
