Re: [gmx-users] Periodic saving of checkpoint file
Hi, Looks OK. The details don't matter, as you are anyway changing ensemble. Mark On Thu, Nov 8, 2018 at 2:39 AM Nicolas Cheron < nicolas.cheron.bou...@gmail.com> wrote: > Hi Mark, > > Thank you for your answer. I didn't know this option. From what I have > read, eneconv is for reading parameters for Nose-Hoover or > Parrinello-Rahman coupling. Thus, if I am doing first an NVT simulation > with the velocity-rescale thermostat or a Langevin dynamics, I don't need > the .edr file, right ? Can you please confirm that this is enough to > prepare the tpr from the time 50ps of the NVT simulation: > > gmx grompp -v -f NVE.mdp -n Index.ndx -o NVE.tpr -c NVT.gro -t NVT.trr > -time 50 -p Protein.top -po NVE_mdout.mdp > > Thank you > > > Le lun. 5 nov. 2018 à 17:50, Mark Abraham a > écrit : > > > Hi, > > > > Since you are anyway intending to change the ensemble, you can just use > > nstxout, nstvout and nstenergy to write output every 10ps. That content > is > > equivalent to that of the checkpoint. Use trjconv and eneconv afterwards > to > > split those up, and use them as inputs to grompp -e -t along with the > > regular inputs. > > > > Mark > > > > On Mon, Nov 5, 2018 at 5:14 PM Nicolas Cheron < > > nicolas.cheron.bou...@gmail.com> wrote: > > > > > Dear all, > > > > > > I would like to run a long NVT simulation and save a checkpoint file > > every > > > 10ps (in order to then run short NVE simulations from each checkpoint). > > Is > > > there a way to save a .cpt file every 10ps in an automatic way? > > > > > > I can do it with other program, for example with Amber "ntwr=-5000" > will > > > save a new restart file every 5000 steps. For now with Gromacs, the > only > > > thing I have found is to write a loop where at each step I extend the > > > simulation time of 10ps with convert-tpr, perform the 10ps simulation, > > save > > > the .cpt, and then loop again. > > > > > > Thanks for your help. > > > > > > Nicolas > > > -- > > > 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. -- 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] Periodic saving of checkpoint file
Hi Mark, Thank you for your answer. I didn't know this option. From what I have read, eneconv is for reading parameters for Nose-Hoover or Parrinello-Rahman coupling. Thus, if I am doing first an NVT simulation with the velocity-rescale thermostat or a Langevin dynamics, I don't need the .edr file, right ? Can you please confirm that this is enough to prepare the tpr from the time 50ps of the NVT simulation: gmx grompp -v -f NVE.mdp -n Index.ndx -o NVE.tpr -c NVT.gro -t NVT.trr -time 50 -p Protein.top -po NVE_mdout.mdp Thank you Le lun. 5 nov. 2018 à 17:50, Mark Abraham a écrit : > Hi, > > Since you are anyway intending to change the ensemble, you can just use > nstxout, nstvout and nstenergy to write output every 10ps. That content is > equivalent to that of the checkpoint. Use trjconv and eneconv afterwards to > split those up, and use them as inputs to grompp -e -t along with the > regular inputs. > > Mark > > On Mon, Nov 5, 2018 at 5:14 PM Nicolas Cheron < > nicolas.cheron.bou...@gmail.com> wrote: > > > Dear all, > > > > I would like to run a long NVT simulation and save a checkpoint file > every > > 10ps (in order to then run short NVE simulations from each checkpoint). > Is > > there a way to save a .cpt file every 10ps in an automatic way? > > > > I can do it with other program, for example with Amber "ntwr=-5000" will > > save a new restart file every 5000 steps. For now with Gromacs, the only > > thing I have found is to write a loop where at each step I extend the > > simulation time of 10ps with convert-tpr, perform the 10ps simulation, > save > > the .cpt, and then loop again. > > > > Thanks for your help. > > > > Nicolas > > -- > > 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.
Re: [gmx-users] Periodic saving of checkpoint file
Hi, Since you are anyway intending to change the ensemble, you can just use nstxout, nstvout and nstenergy to write output every 10ps. That content is equivalent to that of the checkpoint. Use trjconv and eneconv afterwards to split those up, and use them as inputs to grompp -e -t along with the regular inputs. Mark On Mon, Nov 5, 2018 at 5:14 PM Nicolas Cheron < nicolas.cheron.bou...@gmail.com> wrote: > Dear all, > > I would like to run a long NVT simulation and save a checkpoint file every > 10ps (in order to then run short NVE simulations from each checkpoint). Is > there a way to save a .cpt file every 10ps in an automatic way? > > I can do it with other program, for example with Amber "ntwr=-5000" will > save a new restart file every 5000 steps. For now with Gromacs, the only > thing I have found is to write a loop where at each step I extend the > simulation time of 10ps with convert-tpr, perform the 10ps simulation, save > the .cpt, and then loop again. > > Thanks for your help. > > Nicolas > -- > 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] Periodic saving of checkpoint file
Dear all, I would like to run a long NVT simulation and save a checkpoint file every 10ps (in order to then run short NVE simulations from each checkpoint). Is there a way to save a .cpt file every 10ps in an automatic way? I can do it with other program, for example with Amber "ntwr=-5000" will save a new restart file every 5000 steps. For now with Gromacs, the only thing I have found is to write a loop where at each step I extend the simulation time of 10ps with convert-tpr, perform the 10ps simulation, save the .cpt, and then loop again. Thanks for your help. Nicolas -- 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.
