See the Luzar and chandler papers that I believe are mentioned when you run g_hbond -ac. The subtraction is not mentioned in that paper, however.
Erik 17 jun 2011 kl. 06.59 skrev bipin singh: > Thanks Sir,for your reply... > I have a silly question regarding the g_hbond's autocorrelation output: > The output contains the following four columns > (i) Ac fin sys(t) > (ii) Ac(t) > (iii) Cc contact,hb(t) > (iv) -dAc fs/dt > > As I understood the first column is the acf with background > subtraction,and the second column is acf without > background subtraction.....Can you please refer some text from where I > could get the details about the above > mentioned output options and their importance in in H-bond dynamics. > > On Tue, Jun 14, 2011 at 16:53, Erik Marklund <er...@xray.bmc.uu.se> wrote: >> Could be. But, if memory serves me right, there's another dataset in the >> output, which shows the acf without the "background subtraction". >> >> Erik >> >> 14 jun 2011 kl. 12.10 skrev bipin singh: >> >>> I am using the Gromacs 4.5.3........is that feature is present in >>> this version...... >>> >>> On Mon, Jun 13, 2011 at 21:39, Erik Marklund <er...@xray.bmc.uu.se> wrote: >>>> Hi, >>>> >>>> The problem is that g_hbond subtracts a "background level" to compensate >>>> for the finite size of the system. I thought that feature had been taken >>>> away, however. Are you using old code? >>>> >>>> Erik >>>> >>>> 12 jun 2011 kl. 19.33 skrev bipin singh: >>>> >>>>> Hello, >>>>> >>>>> I am calculating the H-bond autocorrelation using g_hbond for my >>>>> system, but after plotting >>>>> I have observed that the value for c(t) is reaching to negative, as >>>>> far as I know it can not be >>>>> negative as the probability can not be negative.......please suggest >>>>> where is the problem...... >>>>> >>>>> -- >>>>> ----------------------- >>>>> Thanks and Regards, >>>>> Bipin Singh >>>>> -- >>>>> 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 >>>> >>>> ----------------------------------------------- >>>> Erik Marklund, PhD student >>>> Dept. of Cell and Molecular Biology, Uppsala University. >>>> Husargatan 3, Box 596, 75124 Uppsala, Sweden >>>> phone: +46 18 471 4537 fax: +46 18 511 755 >>>> er...@xray.bmc.uu.se >>>> http://www2.icm.uu.se/molbio/elflab/index.html >>>> >>>> -- >>>> 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 >>>> >>> >>> >>> >>> -- >>> ----------------------- >>> Regards, >>> Bipin Singh >>> -- >>> 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 >> >> ----------------------------------------------- >> Erik Marklund, PhD student >> Dept. of Cell and Molecular Biology, Uppsala University. >> Husargatan 3, Box 596, 75124 Uppsala, Sweden >> phone: +46 18 471 4537 fax: +46 18 511 755 >> er...@xray.bmc.uu.se >> http://www2.icm.uu.se/molbio/elflab/index.html >> >> -- >> 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 >> > > > > -- > ----------------------- > Regards, > Bipin Singh > > > > -- > ----------------------- > Regards, > Bipin Singh > -- > 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 ----------------------------------------------- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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
