Re: [gmx-users] Forces in source code
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 listgmx-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
RE: [gmx-users] Forces in source code
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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Forces in source code
On 2010-12-11 22.52, Петр Попов wrote: Hello, dear gmx-users. I want to decompose PMF, but I can't use -rerun option for this decompose into what? 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? Best regards, Petr. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
Re: [gmx-users] Forces in source code
To protein-protein and protein-lipid components, for example. 2010/12/12 David van der Spoel sp...@xray.bmc.uu.se: On 2010-12-11 22.52, Петр Попов wrote: Hello, dear gmx-users. I want to decompose PMF, but I can't use -rerun option for this decompose into what? 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? Best regards, Petr. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 listgmx-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
Re: [gmx-users] Forces in source code
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 listgmx-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
