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
