Hi Mark Actually the simulation I am talking about is an annealing simulation in which the system are being annealed from room temperature to 400 k during a 80 ns simulation and then the temperature are being ramped down again to be at room temperature at 100 ns. Now I just want to keep continuing the annealing from 80 ns (keeping the temperature at 400 k) instead of ramping down. And If I start a completely brand new simulation the way you mentioned, it does not continue the simulation at the annealed temperature of my previous simulation. I wish the state.cpt was also truncate-able likes the xtc and trr files to have all at 80 ns.
Regards, Alex On Mon, Jun 24, 2019 at 5:41 AM Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Mon., 24 Jun. 2019, 11:21 Alex, <alexanderwie...@gmail.com> wrote: > > > Thanks Mark. > > With not be able to append to the simulation files, you mean, I should > not > > use the "-cpi state.cpt" in the gmx mdrun, right? > > > No, I mean you can't use -append. You have no relevant file for -cpi. > > > If > > > so, then, the > > simulation is a completely brand new simulation excepts that it use -c > > case.80ns.gro file as starting frame from t = 0.0. Then does the > > trjcat/eneconv used for later concatenation know that the new outputs > > should be assigned to the time t = 8000*1*? > > > > The link I gave earlier has hints for how to prepare for this to go > smoothly. > > In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything > > are being continued from t = 100000. > > > > Yes > > Mark > > > > Thank you. > > Alex > > > > On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > No, that isn't meaningful. Follow > > > > > > > > > http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart > > > but > > > for the -c option, pass a file containing the desired frame extracted > > from > > > your .trr file. You will not be able to append to the simulation files, > > but > > > once the simulation is complete, you can concatenate all the files with > > > trjcat/eneconv. > > > > > > Mark > > > > > > On Sun, 23 Jun 2019 at 22:53, Alex <alexanderwie...@gmail.com> wrote: > > > > > > > Dear all, > > > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > > > > case.100ns.cpt ... all are here, I want to truncate the xtc file at > 80 > > > ns > > > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr > file. > > > > Everything is clear for me except the case.cpt file for which is not > > > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > > > > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > > > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > > > > > > > Thank you. > > > > Alex > > > > -- > > > > 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. > -- 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.
