Hi all, This is more of a question about where I should make a suggestion for the developers. It turns out that Gromacs pull code was designed nearly perfectly to do simulated friction force microscopy (FFM), i.e. scanning a surface with a tip. The only thing that's missing is that the equation of motion for the pulled group's COM does not contain an artificial damping term and the group is free to oscillate, which is a common occurrence in underdamped situations even experimentally. For pulling in systems GMX was designed for, the lack of additional damping makes perfect sense for things that are immersed in solvents (which would readily provide any damping), but most simulated FFM is in vacuum. Options other than umbrella are physically flawed, unfortunately.
Would it had to add a damping term for the umbrella and where should I post this request for the developers? Thank you, Alex -- 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.