Hi, I have a question about the H-bonding autocorrelation function, if I have a trajectory, say 1-1-1-1-1-1-0-1 (1 is H-bonding, 0 is no H-bonding), the time step is 0.006 ps, the correlation is equal to <h(0)h(t)> / <h(0)*h(0)>, my answer is
at t = 0.006, correlation = 7/7 = 1; at t = 0.012, correlation = 5/7 = 0.714; at t = 0.018, correlation = 5/7 = 0.714; at t = 0.024, correlation = 4/7 = 0.571; at t = 0.03, correlation = 3/7 = 0.429; at t = 0.036, correlation = 2/7. = 0.286, at t = 0.042, correlation = 1./7. = 0.143, at t = 0.048, correlation = 1./7. = 0.143, at t = 0.054, correlation = 0. However, when i check gromacs, I found it gives a different answer, here is the command I use "g_hbond -s md.tpr -f new.gro -ac -dist -temp 400 -b 72.444 -e 72.486 -dt 0.006", it uses only the time between 72.444 and 72.486 ps with a timestep of 0.006 ps, and the following is the h-bond number file obtained from gromacs, time (ps) H-bond ( H-bond without angle requirement) 72.444 1 1 72.45 1 1 72.456 1 1 72.462 1 1 72.468 1 1 72.474 1 1 72.48 0 2 72.486 1 1 and the hbac gives , time (ps) C(t) 0 1 0.0059967 0.972222 0.012001 0.933333 the following is from hbac.xvg, @ s0 legend "Ac\sfin sys\v{}\z{}(t)" @ s1 legend "Ac(t)" @ s2 legend "Cc\scontact,hb\v{}\z{}(t)" @ s3 legend "-dAc\sfs\v{}\z{}/dt" 0 1 1 0 235.274 0.0059967 0.411764 0.972222 -9.93411e-09 117.637 0.012001 -0.411764 0.933333 0.166667 -0 Am my calculation wrong? Can anyone help me to resolve this? Thanks! Thanks! Fangyong -- 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.