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.
