[gmx-users] -t option?
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.
Re: [gmx-users] -t option?
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 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.
Re: [gmx-users] -t option?
Thanks Mehdi, Best, Hadi On Wed, Sep 18, 2019 at 12:38 PM Mahdi Bagherpoor 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 > 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.
Re: [gmx-users] -t option?
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 > 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 >> 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.
Re: [gmx-users] -t option?
Thank you Peter, Best, Hadi On Thu, Sep 19, 2019 at 8:29 AM Peter Kroon 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 > > > 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.
