I commented out the 'read_next_x' routine and in place of it i added 'read_next_frame' as given below will that work? Now if i install will i get the trajectory? Is API available for gromacs? Thank you.
write_trx(out,natoms,swi,&top.atoms,0,t,box,x,NULL); } /* } while(read_next_x(status,&t,natoms,x,box)); */ } while(read_next_frame(status,&fr)); close_trj(status); if (out != -1) close_trx(out); if (fp) ffclose(fp); thanx(stderr); return 0; } On Mon, Nov 2, 2009 at 9:41 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > Ramachandran G wrote: >> >> 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. > > It seems likely to be straightforward to change the main loop of > gmx_trjorder to use read_next_frame, which will permit it to read and write > velocities and forces if they are present. I don't have time to do it, > though. > > Mark > >> On Mon, Nov 2, 2009 at 6:36 PM, Mark Abraham <mark.abra...@anu.edu.au> >> 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 >>>> <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 >>>>> >>>> >>>> >>> _______________________________________________ >>> 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