Hi everyone, I'm trying to implement time-varying charges for various ions located in ions.itp in GROMACS 4.5.4, but I'm not sure where to begin.
I've already had some luck implementing AC external electric fields by modifying /src/mdlib/sim_util.c, but this required minimal work from me and a few strategically placed cosines. I have a feeling though that time-varying individual atomic charges will be considerably more difficult since I imagine GROMACS only reads from topol.top (and thus from ions.itp) just once at the beginning without updating the value, so I would likely have to import the time variable and recalculate the charge at every successive step. Since time is explicitly mentioned in the calc_f_el routine of sim_util.c (when I was dealing with external fields) I had no problems making this work there, but is it possible (or practical) to do the same thing with my static atomic charges as well? I've found some references to reading topol.top in /src/kernel/topio.c, and in theory I'd like to import, update, and export certain charges as a function of time, perhaps also in sim_util.c? I just don't know which files or variables to start importing in, or where the best place to implement this would be. Any ideas on this would be greatly appreciated, even if it's just keywords or significant variables for me to grep. Thanks, Zach -- 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
