Yes, i do write velocities to output trajectory at 10 fs. But i understood from the thread(below link) that 'trjorder' do not save the velocities....
http://oldwww.gromacs.org/pipermail/gmx-users/2003-May/005681.html I don't know is there any other way we can do it in the new version. Thanks. Rama On Mon, Nov 2, 2009 at 6:36 PM, Mark Abraham <[email protected]> wrote: > Ramachandran G wrote: >> >> 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. > > First, your .mdp must specify the recording of velocities. Then consult the > documentation for trjorder and g_velacc for what you want. > > Mark > >> On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel >> <[email protected]> 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 >>>> <[email protected]> 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 >>>>>> <[email protected]> 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 >>>>>>>> <[email protected]> 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 >>>>>>>>>> <[email protected]> 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 [email protected] >>>>>>>>>>>> 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 [email protected]. >>>>>>>>>>>> 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. >>>>>>>>>>> [email protected] [email protected] >>>>>>>>>>> http://folding.bmc.uu.se >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> gmx-users mailing list [email protected] >>>>>>>>>>> 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 [email protected]. >>>>>>>>>>> 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. >>>>>>>>> [email protected] [email protected] >>>>>>>>> http://folding.bmc.uu.se >>>>>>>>> _______________________________________________ >>>>>>>>> gmx-users mailing list [email protected] >>>>>>>>> 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 [email protected]. >>>>>>>>> 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. >>>>>>> [email protected] [email protected] http://folding.bmc.uu.se >>>>>>> _______________________________________________ >>>>>>> gmx-users mailing list [email protected] >>>>>>> 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 [email protected]. >>>>>>> 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. >>>>> [email protected] [email protected] http://folding.bmc.uu.se >>>>> _______________________________________________ >>>>> gmx-users mailing list [email protected] >>>>> 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 [email protected]. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>>> >>>> >>>> >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
