I have used the option as follows: g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg
To find the continious HB-correlation function, what option should i need to use. Thank you for your help. Rama On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Ramachandran G wrote: >> >> 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: > > You need to pass the -life option. > >> >> >> ----------------------------------------------------------------------------------------------------------------------------------------- >> 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 >>> >> >> >> > > > -- > 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