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Hi,<br><br>Note that it is impossible to decompose a free energy (difference), which a PMF is,<br>uniquely into different energy or force components.<br>A free energy is not simply the sum of energy terms, but is the result of how<br>different energy terms together affect the accessible phase space.<br>The effect on a free energy of two energy terms is usually not simply the sum<br>of the two effects.<br><br>Berk<br><br>> Date: Mon, 13 Dec 2010 01:09:01 +0300<br>> Subject: Re: [gmx-users] Forces in source code<br>> From: magistrpetrus@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> Thank You!<br>> I'll try to get what you writed, so, perhaps, I'll write about my<br>> success or its lack!<br>> <br>> 12 декабря 2010 г. 4:42 пользователь Mark Abraham<br>> <mark.abraham@anu.edu.au> написал:<br>> ><br>> ><br>> > On 12/12/10, Петр Попов <magistrpetrus@gmail.com> wrote:<br>> ><br>> > Hello, dear gmx-users.<br>> ><br>> > I want to decompose PMF, but I can't use -rerun option for this<br>> > because I get this PMF due to pull force. And also .trr files are<br>> > large to do md with different energy groups to get PMF.<br>> > So, I need to adopt source code for this task.<br>> > Could you help me and give me any advices? - in what .c files are<br>> > forces and pull force are evaluated? Or from what I must start?<br>> ><br>> > To do this kind of group-wise decomposition of forces you need to give<br>> > different force arrays to the evaluation of different neighbour lists. I've<br>> > posted replies to this before, so please search for it. To get a handle on<br>> > how things work, set up a tiny box of water molecules using a plain Coulomb<br>> > cut-off and step through a serial GROMACS mdrun in a debugger. Then move the<br>> > simulation gradually closer to the setup you have in mind and note the<br>> > differences in how the force arrays are handled - they'll be different in<br>> > parallel and presumably with pulling. Then you'll have to mimic the way the<br>> > ebin code stores group-wise non-bonded energies to store group-wise<br>> > non-bonded forces. Then you'll want to write them out to separate .trr<br>> > files.<br>> ><br>> > Mark<br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at<br>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> ><br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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