You need -on for gmx select to write out the index file. On Thu, Apr 12, 2018 at 8:48 AM, Dilip.H.N <cy16f01.di...@nitk.edu.in> wrote:
> I tried the following two ways ie., with gmx select and with gmx trjorder > > 1) when i give the command :- > gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro -nshell > -r 0.35 > > i got an output file, it has all the water molecules (i have 511 water > molecules in my system) for each time frame but it has arranged according > to the smallest distance to atoms in the reference group. (but i want only > those water molecules within 0.35nm of nitrogen of glycine molecule.) > > 2) in this command:- > gmx select -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -oi -select '"close to > name N" resname SOL and within 0.35 of group protein' > > i am getting an .dat file which has only the coordinates and the format on > as in index file format. > > Actually, i wanted the format in which the gmx trjorder output gives (as in > my case, order.gro), but i want only those water molecules which are within > 3.5 nm of the nitrogen atom of glycine molecule for each time frame. > > Any suggestions are appreciated. > > Thank you. > > > <https://mailtrack.io/> Sent with Mailtrack > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign= > signaturevirality&> > > --- > With Best Regards, > > Dilip.H.N > PhD Student. > > On Wed, Apr 11, 2018 at 6:23 PM, Marc Hoemberger <hoemb...@brandeis.edu> > wrote: > > > You can use either gmx trjorder with the nshell parameter (if it is as > > simple as within Xnm of Y, use nshell parameter, see manual) or gmx > select > > (if you need some more complex selection). > > > > On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N <cy16f01.di...@nitk.edu.in> > > wrote: > > > > > Hello all, > > > > > > I want to get the water molecules which are at a certain distance (say > > all > > > the water molecules which are within 0.35nm of the Nitrogen atom of > > glycine > > > molecule). How can i get this all the coordinates.? > > > > > > Any specific commands..?? > > > > > > > > > Thank you. > > > > > > --- > > > With Best Regards, > > > > > > Dilip.H.N > > > PhD Student. > > > <https://mailtrack.io/> Sent with Mailtrack > > > <https://mailtrack.io?utm_source=gmail&utm_medium= > > signature&utm_campaign= > > > signaturevirality&> > > > -- > > > 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. > > > > > > > > > > > -- > > Marc Hoemberger > > Ph.D. Candidate, Biochemistry and Biophysics, > > Laboratory of Dorothee Kern > > MS-009, 415 South St. > > Brandeis University > > Waltham, MA, 02453 > > -- > > 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. > > > -- > 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. -- Joe Jordan -- 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.