On Fri, Nov 19, 2010 at 12:15, Reiner Ribarics <[email protected]> wrote: > Our group has already done some rather long simulations and according to the > script files forces are written every 10000 steps and can be accessed via > trjconv with -cf option that assigns each atom a temperature factor. I was > wondering if that is the way gromacs stores the forces in the trajectory > file. Or are the temperature factors calculated from other (maybe pairwise) > forces?
It's not clear to me what you try to do. Obtain atomic forces ? Obtain pairwise forces ? Know the format in which forces are stored in the trajectory file ? Something else entirely ? > I also had a look at FDA gromacs that is able to write out pairwise forces, > but unfortunately it falls back on the rather slow gromacs routines and we > want to avoid rerunning our simulations if possible. Then please take a look again. The forces are indeed saved by hooking into the C kernels, but in a 'mdrun -rerun' phase which reads back the trajectory and writes the forces, which avoids having a compute intensive phase with the C kernels and the FDA modifications. Kind regards, Bogdan -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
