[gmx-users] calculating the pmf in constrained force simulations
Do you mean that you do constrained position simulations and want to know how to process the force? If so, read about thermodynamic integration (TI). I mostly work with US and position restraints, but for absolute constraints I believe that you should take the average force at each constrained position and do a trapezoidal integration of the mean force. Surely somebody has written a paper on this that you can read. Chris. -- original message -- Hi I do constrained force simulations and i have the pullf.xvg and pullx.xvg files.. I want to know how to calculate the force for each simulation and i how to integrate the forces.. can some one help me. -- 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] calculating the pmf in constrained force simulations
yes exactly thats what I am trying to do.. Thanks a lot for the suggestion Ramya On Sat, Nov 26, 2011 at 7:26 AM, chris.ne...@utoronto.ca wrote: Do you mean that you do constrained position simulations and want to know how to process the force? If so, read about thermodynamic integration (TI). I mostly work with US and position restraints, but for absolute constraints I believe that you should take the average force at each constrained position and do a trapezoidal integration of the mean force. Surely somebody has written a paper on this that you can read. Chris. -- original message -- Hi I do constrained force simulations and i have the pullf.xvg and pullx.xvg files.. I want to know how to calculate the force for each simulation and i how to integrate the forces.. can some one help me. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://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] calculating the pmf in constrained force simulations
Hi I do constrained force simulations and i have the pullf.xvg and pullx.xvg files.. I want to know how to calculate the force for each simulation and i how to integrate the forces.. can some one help me. Ramya -- 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
