Hi, Constructing a .tpr is covered many GROMACS tutorials you can find. What is particular about your case that you do not have one from doing the simulation?
Mark On Mon, Dec 23, 2013 at 9:40 AM, Rasoul Nasiri <nasiri1...@gmail.com> wrote: > Many thanks Tsjerk, > > Let me ask another question. As you know in most cases of analysis, one > needs to have tpr file along with the trajectory. > How can I construct it? The potential that I'm using in my MD simulations > is ReaxFF (a reactive FF). > > Best, > Rasoul > > > On Sun, Dec 22, 2013 at 9:21 AM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > > > Hi Raoul, > > > > You can also convert it to .gro or .pdb and do the analysis on that. > > Scriptwise that's trivial. > > > > Cheers, > > > > Tsjerk > > > > > > On Sat, Dec 21, 2013 at 10:12 PM, Rasoul Nasiri <nasiri1...@gmail.com > > >wrote: > > > > > Dear all, > > > > > > Is there any available script/Tcl in order to convert a x,y,z > trajectory > > > (x,y,z-coordinates+velocities) to *.trr one? > > > > > > I have optained the following trajectory and I need to have *.trr for > > > analysing of my MD; > > > > > > > > > C 45.96903 21.49863 24.62913 0.00000 0.00000 > > > 0.00000 > > > H 47.06603 21.49863 24.62913 0.00000 0.00000 > > > 0.00000 > > > H 45.80503 22.58663 24.62913 0.00000 0.00000 > > > 0.00000 > > > H 45.56903 21.09663 25.55113 0.00000 0.00000 > > > 0.00000 > > > C 45.38203 20.69563 23.47013 0.00000 0.00000 > > > 0.00000 > > > H 45.90103 19.74763 23.37813 0.00000 0.00000 > > > 0.00000 > > > H 45.64903 21.18663 22.53113 0.00000 0.00000 > > > 0.00000 > > > C 43.87003 20.45463 23.58413 0.00000 0.00000 > > > 0.00000 > > > . > > > . > > > . > > > . > > > > > > Any help is highly appreciated. > > > > > > Best, > > > Rasoul > > > -- > > > 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. > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > 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.
