Thanks for your replies. 1- I need bond and charge info along with position and velocity ones. All change during the MD simulation required a reactive force field rather than traditional one.
2- How one can construct a tpr for a system in which bonds/charges change when it's evolved? Best, Rasoul On Mon, Dec 23, 2013 at 9:30 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Also, consider what you need it for. If you only need atom/residue > information and/or reference coordinates, a .gro/.pdb file will do. Only if > you need to have bonds/masses/charges/... you really need a .tpr file for > reference. > > Cheers, > > Tsjerk > > > On Mon, Dec 23, 2013 at 4:00 AM, Mark Abraham <mark.j.abra...@gmail.com > >wrote: > > > 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-usersor > > > > > 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-usersor > > > > 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. > > > > > > -- > 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.