Thank you Peter, Best, Hadi On Thu, Sep 19, 2019 at 8:29 AM Peter Kroon <p.c.kr...@rug.nl> wrote:
> Hi Hadi, > > > to expand a little on Mahdi's (correct) answer: > > The checkpoint file contains coordinates and velocities in full > precision (unlike .gro and .xtc files). In addition, it contains the > state of the thermostat and barostat (if applicable). The > thermo/barostat states are not present in the gro/mdp/tpr files, since > they depend on the history of your system. Because of this, including > the checkpoint file to continue your simulation is always a good idea. > > See also: `gmx mdrun -h` and `gmx grompp -h`. > > > Peter > > On 19-09-19 05:13, Hadi Rahmaninejad wrote: > > Thanks Mehdi, > > > > Best, > > Hadi > > > > On Wed, Sep 18, 2019 at 12:38 PM Mahdi Bagherpoor <mehdi.bp...@gmail.com > > > > wrote: > > > >> Hi Hadi, > >> > >> It is well explained in Gromacs tutorial, in the below: > >> http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html > >> > >> "Note that we are now including the -t flag to include the checkpoint > file > >> from the *NVT* equilibration" > >> > >> Cheers, > >> Mahdi > >> On Wed, Sep 18, 2019 at 5:43 PM Hadi Rahmaninejad < > ha.rahma...@gmail.com> > >> wrote: > >> > >>> Hello dear users, > >>> > >>> I am going to run a simulation according to a tutorial, but there is an > >>> option of "-t nvt.cpt" that I don't know what is it, and I couldn't > find > >>> any explanation for that. I appreciate if any of you can give me a > short > >>> description of what is that doing, > >>> > >>> Best wishes, > >>> Hadi > >>> -- > >>> 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.