Dear Gromacs users, I would like to perform targeted molecular dynamics with gromacs. I have read all the post concerning it and I can do it with position restraints by putting the final conformation in the -r option of grompp. But this is not a "real TMD". Indeed, in TMD, the force applied to the structure is dependent of the RMSD in order to have a constant RMSD decrease. Here the force is constant. So, when the starting conformation is far from the final conformation the RMSD decreases quickly but when it's near the final conformation, the force constant can be not enought and the final conformation can be never reached (unless putting a big force).
I see in the manual in the paragraph 6.4 that it's possible to do TMD with the free energy options and the -r -and -rb options of grompp. Nevertheless, none example is available for the mdp input file. How i can do it please? Thank you Landraille -- View this message in context: http://gromacs.5086.n6.nabble.com/TMD-using-free-energy-code-tp5006260.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
