Thank You! I'll try to get what you writed, so, perhaps, I'll write about my success or its lack!
12 декабря 2010 г. 4:42 пользователь Mark Abraham <mark.abra...@anu.edu.au> написал: > > > On 12/12/10, Петр Попов <magistrpet...@gmail.com> wrote: > > Hello, dear gmx-users. > > I want to decompose PMF, but I can't use -rerun option for this > because I get this PMF due to pull force. And also .trr files are > large to do md with different energy groups to get PMF. > So, I need to adopt source code for this task. > Could you help me and give me any advices? - in what .c files are > forces and pull force are evaluated? Or from what I must start? > > To do this kind of group-wise decomposition of forces you need to give > different force arrays to the evaluation of different neighbour lists. I've > posted replies to this before, so please search for it. To get a handle on > how things work, set up a tiny box of water molecules using a plain Coulomb > cut-off and step through a serial GROMACS mdrun in a debugger. Then move the > simulation gradually closer to the setup you have in mind and note the > differences in how the force arrays are handled - they'll be different in > parallel and presumably with pulling. Then you'll have to mimic the way the > ebin code stores group-wise non-bonded energies to store group-wise > non-bonded forces. Then you'll want to write them out to separate .trr > files. > > Mark > -- > gmx-users mailing list gmx-us...@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 > -- 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
