Re: [gmx-users] Extending a program
No its not needed. gmx convert-tpr will serve the perpose. In -extend option you can specify the extension (50ns/100ns). On Thu, Feb 23, 2017 at 4:33 PM, RAHUL SURESH wrote: > Okay > > In case I need to extend another 50ns should change mdp? > > > > On Thu, 23 Feb 2017 at 3:21 PM, Tasneem Kausar > wrote: > > > If you have state.cpt file from the previous simulation, on extending the > > simulation -cpi state.cpt will serve to read the last coordinate of your > > previous simulation. > > Use this command > > gmx mdrun -v -deffnm extend.tpr -cpi state.cpt > > > > On Thu, Feb 23, 2017 at 12:24 PM, RAHUL SURESH > > wrote: > > > > > dear Amir > > > it is mandatory to change the mdp file? > > > > > > And what change should i do in that? > > > > > > On Thu, Feb 23, 2017 at 12:20 PM, Amir Zeb > wrote: > > > > > > > Hello Rahul, > > > > > > > > Just extend the simulation time in mdp file and repeat the same > > commands > > > as > > > > you done for early 100 ns. > > > > > > > > Best! > > > > > > > > On Wed, Feb 22, 2017 at 10:47 PM, RAHUL SURESH < > > drrahulsur...@gmail.com> > > > > wrote: > > > > > > > > > I have a 100ns simulated file.(md.xtc) I need to extend to another > > 100 > > > > ns. > > > > > > > > > > do i need to make any change to mdp file.? > > > > > > > > > > I used the command > > > > > > > > > > > > > > > > > > > > *gmx convert-tpr -s md.xtc -extend 10 -o extend.tpr* > > > > > > > > > > *gmx mdrun -v -deffnm extend.tpr* > > > > > > > > > > > > > > > -- > > > > > *Regards,* > > > > > *Rahul Suresh* > > > > > *Research Scholar* > > > > > *Bharathiar University* > > > > > *Coimbatore* > > > > > -- > > > > > 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. > > > > > > > > > > > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > 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. > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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] Extending a program
Okay In case I need to extend another 50ns should change mdp? On Thu, 23 Feb 2017 at 3:21 PM, Tasneem Kausar wrote: > If you have state.cpt file from the previous simulation, on extending the > simulation -cpi state.cpt will serve to read the last coordinate of your > previous simulation. > Use this command > gmx mdrun -v -deffnm extend.tpr -cpi state.cpt > > On Thu, Feb 23, 2017 at 12:24 PM, RAHUL SURESH > wrote: > > > dear Amir > > it is mandatory to change the mdp file? > > > > And what change should i do in that? > > > > On Thu, Feb 23, 2017 at 12:20 PM, Amir Zeb wrote: > > > > > Hello Rahul, > > > > > > Just extend the simulation time in mdp file and repeat the same > commands > > as > > > you done for early 100 ns. > > > > > > Best! > > > > > > On Wed, Feb 22, 2017 at 10:47 PM, RAHUL SURESH < > drrahulsur...@gmail.com> > > > wrote: > > > > > > > I have a 100ns simulated file.(md.xtc) I need to extend to another > 100 > > > ns. > > > > > > > > do i need to make any change to mdp file.? > > > > > > > > I used the command > > > > > > > > > > > > > > > > *gmx convert-tpr -s md.xtc -extend 10 -o extend.tpr* > > > > > > > > *gmx mdrun -v -deffnm extend.tpr* > > > > > > > > > > > > -- > > > > *Regards,* > > > > *Rahul Suresh* > > > > *Research Scholar* > > > > *Bharathiar University* > > > > *Coimbatore* > > > > -- > > > > 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. > > > > > > > > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] Extending a program
If you have state.cpt file from the previous simulation, on extending the simulation -cpi state.cpt will serve to read the last coordinate of your previous simulation. Use this command gmx mdrun -v -deffnm extend.tpr -cpi state.cpt On Thu, Feb 23, 2017 at 12:24 PM, RAHUL SURESH wrote: > dear Amir > it is mandatory to change the mdp file? > > And what change should i do in that? > > On Thu, Feb 23, 2017 at 12:20 PM, Amir Zeb wrote: > > > Hello Rahul, > > > > Just extend the simulation time in mdp file and repeat the same commands > as > > you done for early 100 ns. > > > > Best! > > > > On Wed, Feb 22, 2017 at 10:47 PM, RAHUL SURESH > > wrote: > > > > > I have a 100ns simulated file.(md.xtc) I need to extend to another 100 > > ns. > > > > > > do i need to make any change to mdp file.? > > > > > > I used the command > > > > > > > > > > > > *gmx convert-tpr -s md.xtc -extend 10 -o extend.tpr* > > > > > > *gmx mdrun -v -deffnm extend.tpr* > > > > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > 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. > > > > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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] Extending a program
dear Amir it is mandatory to change the mdp file? And what change should i do in that? On Thu, Feb 23, 2017 at 12:20 PM, Amir Zeb wrote: > Hello Rahul, > > Just extend the simulation time in mdp file and repeat the same commands as > you done for early 100 ns. > > Best! > > On Wed, Feb 22, 2017 at 10:47 PM, RAHUL SURESH > wrote: > > > I have a 100ns simulated file.(md.xtc) I need to extend to another 100 > ns. > > > > do i need to make any change to mdp file.? > > > > I used the command > > > > > > > > *gmx convert-tpr -s md.xtc -extend 10 -o extend.tpr* > > > > *gmx mdrun -v -deffnm extend.tpr* > > > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] Extending a program
Hello Rahul, Just extend the simulation time in mdp file and repeat the same commands as you done for early 100 ns. Best! On Wed, Feb 22, 2017 at 10:47 PM, RAHUL SURESH wrote: > I have a 100ns simulated file.(md.xtc) I need to extend to another 100 ns. > > do i need to make any change to mdp file.? > > I used the command > > > > *gmx convert-tpr -s md.xtc -extend 10 -o extend.tpr* > > *gmx mdrun -v -deffnm extend.tpr* > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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.
[gmx-users] Extending a program
I have a 100ns simulated file.(md.xtc) I need to extend to another 100 ns. do i need to make any change to mdp file.? I used the command *gmx convert-tpr -s md.xtc -extend 10 -o extend.tpr* *gmx mdrun -v -deffnm extend.tpr* -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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.
