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 <mark.j.abra...@gmail.com> 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.