Hi, Note that it is impossible to decompose a free energy (difference), which a PMF is, uniquely into different energy or force components. A free energy is not simply the sum of energy terms, but is the result of how different energy terms together affect the accessible phase space. The effect on a free energy of two energy terms is usually not simply the sum of the two effects.
Berk > Date: Mon, 13 Dec 2010 01:09:01 +0300 > Subject: Re: [gmx-users] Forces in source code > From: magistrpet...@gmail.com > To: gmx-users@gromacs.org > > 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-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 > > > -- > 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
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