Thank You On Fri, Sep 22, 2017 at 1:35 PM, Erik Marklund <erik.markl...@kemi.uu.se> wrote:
> Dear Tsaneem, > > Negative values don’t signify lack of correlation, but anticorrelation. > Also, by omitting negative values you introduce a slight bias in your fit > towards longer half-life. > > Kind regards, > Erik > ______________________________________________ > Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow > Department of Chemistry – BMC, Uppsala University > +46 (0)18 471 4539 > erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> > > On 22 Sep 2017, at 06:18, Tasneem Kausar <tasneemkausa...@gmail.com< > mailto:tasneemkausa...@gmail.com>> wrote: > > Thank you for reply > > I read the references and I know that one of the columns of g_hbond output > is without subtraction > and the value ranges between 0 to 1. The only help I need is that can I > fit the curve of the first column (which has negative value) and neglect > the range of curve of negative part while fitting to get the exponential > parameters of the curve. This seems to me reasonable only for getting > information parameter as negative ACF value mean no correlation parameter. > > Any help will be appreciated. > > Thanks in Advance. > > On Thu, Sep 21, 2017 at 2:54 PM, Erik Marklund <erik.markl...@kemi.uu.se< > mailto:erik.markl...@kemi.uu.se>> > wrote: > > Dear Tasneem, > > Quite often ACF calculations involve subtraction of the average signal, > and this normally renders some negative values in the ACF. It’s been a bit > too long since I dealt with the gmx hbond code, but I suspect that is what > is going on here. I suggest reading the references that gmx hbond mentions, > where the four quantities in the output are defined. > > Kind regards, > Erik > ______________________________________________ > Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow > Department of Chemistry – BMC, Uppsala University > +46 (0)18 471 4539 > erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto: > erik.markl...@kemi.uu.se> > > On 21 Sep 2017, at 11:12, Tasneem Kausar <tasneemkausa...@gmail.com< > mailto:tasneemkausa...@gmail.com>< > mailto:tasneemkausa...@gmail.com>> wrote: > > Still waiting for suggestions. > > On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar <tasneemkausa...@gmail.com > <mailto:tasneemkausa...@gmail.com> > <mailto:tasneemkausa...@gmail.com>> > wrote: > > Dear all > > I want to calculate residence time of interface water molecules at protein > interface. I am using Gromacs-4.6.4. > I am using using following command > g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac > protein_ac.xvg -contact > In the index file there are protein interface residues and 8 water > molecule that are present at the protein interface. I have selected protein > interface and 8 water for calculation. In the output of autocorrelation > there are four y axis columns. I came through reply of Erik. He mentioned > the effect of periodic boundary condition on the output. In my case first y > axis has several negative values. I want to do an exponential fit with > function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the > negative values of the output file? If yes what is the reason to do that. > If I am wrong please suggest me to do the right way to obtain residence > time. > > > Thanks in Advance > > Tasneem Kausar > > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org<mailto:gmx-users-request@ > gromacs.org><mailto:gmx-users-request@ > gromacs.org<http://gromacs.org/>>. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org<mailto:gmx-users-request@ > gromacs.org>. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org<mailto:gmx-users-request@ > gromacs.org>. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.