Re: [gmx-users] conversion of X,Y,Z + velocities to *.trr
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 24.629130.00.0 0.0 H 47.06603 21.49863 24.629130.00.0 0.0 H 45.80503 22.58663 24.629130.00.0 0.0 H 45.56903 21.09663 25.551130.00.0 0.0 C 45.38203 20.69563 23.470130.00.0 0.0 H 45.90103 19.74763 23.378130.00.0 0.0 H 45.64903 21.18663 22.531130.00.0 0.0 C 43.87003 20.45463 23.584130.00.0 0.0 . . . . 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
Re: [gmx-users] conversion of X,Y,Z + velocities to *.trr
On Mon, Dec 23, 2013 at 8:43 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: 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? You can't make a proper .tpr, because the general assumption is that connectivity and charge are within the MM approximation, i.e. constant. You can certainly make one that matches a given configuration, but you'll need to get your hands dirty with a script that can assign (say) partly-formed bonds to be one or the other thing. Mark 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 24.629130.00.0 0.0 H 47.06603 21.49863 24.629130.00.0 0.0 H 45.80503 22.58663 24.629130.00.0 0.0 H 45.56903 21.09663 25.551130.00.0 0.0 C 45.38203 20.69563 23.470130.00.0 0.0 H 45.90103 19.74763 23.378130.00.0 0.0 H 45.64903 21.18663 22.531130.00.0 0.0 C 43.87003 20.45463 23.584130.00.0 0.0 . . . . 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_Listbefore 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-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. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] conversion of X,Y,Z + velocities to *.trr
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.comwrote: 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 24.629130.00.0 0.0 H 47.06603 21.49863 24.629130.00.0 0.0 H 45.80503 22.58663 24.629130.00.0 0.0 H 45.56903 21.09663 25.551130.00.0 0.0 C 45.38203 20.69563 23.470130.00.0 0.0 H 45.90103 19.74763 23.378130.00.0 0.0 H 45.64903 21.18663 22.531130.00.0 0.0 C 43.87003 20.45463 23.584130.00.0 0.0 . . . . 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.
Re: [gmx-users] conversion of X,Y,Z + velocities to *.trr
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 24.629130.00.0 0.0 H 47.06603 21.49863 24.629130.00.0 0.0 H 45.80503 22.58663 24.629130.00.0 0.0 H 45.56903 21.09663 25.551130.00.0 0.0 C 45.38203 20.69563 23.470130.00.0 0.0 H 45.90103 19.74763 23.378130.00.0 0.0 H 45.64903 21.18663 22.531130.00.0 0.0 C 43.87003 20.45463 23.584130.00.0 0.0 . . . . 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.
