[gmx-users] How to read .dat file
I generated a .dat file with the following command: gmx rms -s .pdb -f 1.xtc -f2 2.xtc -n index.ndx -o rms.xvg -m rms.xpm -bin rms.dat But how to read the binary file rms.dat? The reason is that, I found the lowest RMSD in RMSD matrix (rms.xpm) is 0.52 nm; how to know which frame in 1.xtc and which frame in 2.xtc have this minimal RMSD? Thanks, Qing -- 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.
Re: [gmx-users] How to read .dat file
I think this link should be helpful. http://manual.gromacs.org/programs/gmx-rms.html You can have a look at rms.xvg file, it contains rmsd values. Best regards, Dading Huang On Wed, Jun 14, 2017 at 7:05 PM, Qing Lv wrote: > I generated a .dat file with the following command: > gmx rms -s .pdb -f 1.xtc -f2 2.xtc -n index.ndx -o rms.xvg -m rms.xpm > -bin rms.dat > But how to read the binary file rms.dat? > > > The reason is that, > I found the lowest RMSD in RMSD matrix (rms.xpm) is 0.52 nm; how to know > which frame in 1.xtc and which frame in 2.xtc have this minimal RMSD? > > > Thanks, > Qing > -- > 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.
Re: [gmx-users] How to read .dat file
The file rms.xvg contains only RMSD values against the reference PDB structure; what I need to know is the contents of RMSD matrix between 2 trajectories. Qing At 2017-06-15 15:17:08, "Dd H" wrote: >I think this link should be helpful. >http://manual.gromacs.org/programs/gmx-rms.html >You can have a look at rms.xvg file, it contains rmsd values. > >Best regards, >Dading Huang > > >On Wed, Jun 14, 2017 at 7:05 PM, Qing Lv wrote: > >> I generated a .dat file with the following command: >> gmx rms -s .pdb -f 1.xtc -f2 2.xtc -n index.ndx -o rms.xvg -m rms.xpm >> -bin rms.dat >> But how to read the binary file rms.dat? >> >> >> The reason is that, >> I found the lowest RMSD in RMSD matrix (rms.xpm) is 0.52 nm; how to know >> which frame in 1.xtc and which frame in 2.xtc have this minimal RMSD? >> >> >> Thanks, >> Qing >> -- >> 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. -- 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.
