Because in the command gmx h_bond it is not calculating Continuous hydrogen bond correlation function
<https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> On Tue, May 30, 2017 at 10:58 PM, Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > I have ran a simulation and extracted the trajectory for t=0.5 ps each in > gromacs. The trajectory file is as follows.. > > Generated by trjconv : Glycine-Ammonia-Water t= 0.500 > 28SOL OW 115 1.586 0.579 1.240 > 28SOL HW1 116 1.520 0.524 1.293 > 28SOL HW2 117 1.645 0.519 1.187 > 29SOL OW 118 0.135 0.791 1.373 > 29SOL HW1 119 0.168 0.716 1.316 > 29SOL HW2 120 0.190 0.873 1.355 > 30SOL OW 121 0.279 0.419 0.486 > 30SOL HW1 122 0.366 0.400 0.440 > 30SOL HW2 123 0.204 0.415 0.41 > . > . > . > > Generated by trjconv : Glycine-Ammonia-Water t= 1.000 > 28SOL OW 115 1.586 0.579 1.240 > 28SOL HW1 116 1.520 0.524 1.293 > 28SOL HW2 117 1.645 0.519 1.187 > 29SOL OW 118 0.135 0.791 1.373 > 29SOL HW1 119 0.168 0.716 1.316 > 29SOL HW2 120 0.190 0.873 1.355 > 30SOL OW 121 0.279 0.419 0.486 > 30SOL HW1 122 0.366 0.400 0.440 > 30SOL HW2 123 0.204 0.415 0.41 > . > . > . > > Generated by trjconv : Glycine-Ammonia-Water t= 10.000 > 28SOL OW 115 1.586 0.579 1.240 > 28SOL HW1 116 1.520 0.524 1.293 > 28SOL HW2 117 1.645 0.519 1.187 > 29SOL OW 118 0.135 0.791 1.373 > 29SOL HW1 119 0.168 0.716 1.316 > 29SOL HW2 120 0.190 0.873 1.355 > 30SOL OW 121 0.279 0.419 0.486 > 30SOL HW1 122 0.366 0.400 0.440 > 30SOL HW2 123 0.204 0.415 0.41 > . > > Can anybody suggest ideas to write a python program/code to calculate the > hydrogen bond (continuous/intermittent) time correlations..ie., hydrogen > bond if it exists between oxygen of one water molecule with hydrogen of > other water molecule at a distance less than 2.45 angstrom or between > oxygen of one water molecule with oxygen of other water molecule at a > distance less than 3.5 angstrom. > > Any suggestions regarding this... > > Thank you > > > -- > With Best Regards, > > DILIP.H.N > Ph.D Student > > > > <https://mailtrack.io/> Sent with Mailtrack > <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> > -- With Best Regards, DILIP.H.N Ph.D Student -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.