Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later when i checked the trajectory file(ordered.trr) by converting to *.gro file using trjconv, i understood that 'velocities' are missing.
So, can you guide me how i can do velocity auto correlation function for the water molecules exist close to the protein(i.e., in a hydration shell) using gromacs? Thank you again. Regards, Rama On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Ramachandran G wrote: >> >> Dear David, >> Thank you for you help. It is very much helpful for me. >> >> I have one more question. Is it possible to create index file for the >> oxygen atom or water molecules alone exist in a hydration shell. Thank >> you again. >> Rama >> > > You could try the trjorder program > >> On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel >> <sp...@xray.bmc.uu.se> wrote: >> >>> >>> Ramachandran G wrote: >>> >>>> >>>> I have used the option as follows: >>>> g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg >>>> >>> >>> -life koko.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 >>>>> >>>>> >>>> >>>> >>> >>> -- >>> 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 >>> >>> >> >> >> >> > > _______________________________________________ > 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