[gmx-users] g_hbond -ac -life
Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life. Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. Also, I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB lifetime? any help will highly appreciated -- 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] g_hbond -ac -life
shahab shariati skrev 2010-11-24 16.24: Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life. Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. Also, I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB lifetime? any help will highly appreciated For hblife, I don't know. in hbac.xvg the first column is the autocorrelation function (acf) with a (somewhat dubious) correction to compensate for a finite system (the acf sohuld approac zero for large distances, but for a periodic finite system the tail is proprotional to 1/N, N being the number of particles). The second one is the 'raw' acf. Third column is the cross correlation between the hb-existence functions and corresponding contact-existence function (contacts fulfil the distace criterium but not the angular criterium). The fourth column is the derivative of the first column. The problem with -life, as far as I know, is that it models the hbond breaking/formation as a simple one step process, which may not be a good description. See the Luzar and Chandler papers for the theory behind the constants reported by g_hbond -ac. Therefore I'd use -ac to determine the rate for hb breaking. Cheers, -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@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
[gmx-users] g_hbond -ac -life
Dear Erik thanks. thus -ac is only for determine the rate for hb breaking. is it true? or there is other usable case for -ac option? -- 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] g_hbond -ac -life
shahab shariati skrev 2010-11-24 16.45: Dear Erik thanks. thus -ac is only for determine the rate for hb breaking. is it true? or there is other usable case for -ac option? And formation. And equillibrium constant. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@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
