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> On 21 Sep 2017, at 11:12, Tasneem Kausar <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>> 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-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.
