Thank you for the reference. But still i like check it out for my system. But still i don't know how to get 'S' type hydrogen bonding. I am pasting my screen output below:
----------------------------------------------------------------------------------------------------------------------------------------- Checking for overlap in atoms between plane-B and SOL Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms) Found 6650 donors and 19904 acceptors trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Will do grid-seach on 16x16x16 grid, rcut=0.35 Last frame 30000 time 300.000 Found 3304 different hydrogen bonds in trajectory Found 7135 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 6650/6650 - Reduced number of hbonds from 3304 to 3151 - Reduced number of distances from 7135 to 7135 Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2# Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible ACF 3151/3151 Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) > 0.001 Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161 Hydrogen bond thermodynamics at T = 298.15 K -------------------------------------------------- Type Rate (1/ps) Time (ps) DG (kJ/mol) Forward 0.035 28.458 12.829 Backward -0.009 -111.540 -666.000 One-way 0.074 13.435 10.968 Integral 0.047 21.471 12.130 Relaxation 0.047 21.358 12.117 gcq#129: "She's a Good Sheila Bruce" (Monty Python) ----------------------------------------------------------------------------------------------------------------------------------------------- The hydrogen bond Autocorrelation function output has five columns. The first columne is the time axis, i think the second column gives the C(t) other 3 columns i don't understand. Will you please help me to understand thank you. Rama On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Ramachandran G wrote: >> >> C_HB(T) = <h(t)h(T+t)>/ <h(t)> >> >> S_HB(T) = <h(t)H(T+t)>/<h(t)> >> >> >> h(T) = 1, if a pair of atoms bonded at time T, >> = 0, otherwise >> >> H(T) = 1, if a pair of atoms continously bonded >> between time 0 to time T, >> = 0, otherwise >> >> S_HB(t) probes the continuous existence of a hydrogen bond, while >> C_HB(t) allows for >> the reformation of a bond that is broken at some intermediate time. The >> former >> is thus a strict definition of the hydrogen bond lifetime, while the >> latter is more >> permissive. >> >> I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure >> about that. Anybody knows >> please help me. Thank you. > > This is correct. However, the S_HB definition is not very useful, see my > paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The > uninterrupted life time is computed by g_hbond however. Check the screen > output. > >> >> Rama >> >> On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel >> <sp...@xray.bmc.uu.se> wrote: >>> >>> Ramachandran G wrote: >>>> >>>> Dear gromacs users: >>>> I like to know whether gromacs will calculate S-type hydrogen >>>> bond correlation function? >>>> If it so how it can be done? Thank you. >>> >>> What does that mean? >>> >>> >>>> Rama >>>> _______________________________________________ >>>> gmx-users mailing list gmx-us...@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. >>> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >>> _______________________________________________ >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>> >> >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. _______________________________________________ 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/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/mailing_lists/users.php
