Hi, As you can see in gmx help grompp, you should use -t when you want a high fidelity restart. Obviously, then you would not also choose to generate velocities (though I forget what takes priority over the velocities in that case)
Mark On Fri., 20 Sep. 2019, 01:05 Prabir Khatua, <prabir07c...@gmail.com> wrote: > Thank you very much Mark! > > I could see that the velocities exactly match with what was there in the > initial .gro file that was used with -f option. > This means that -t option is optional in this case provided one uses > gen_vel as no. I am still confused when one > should use -t option. Is it like -t option ensures to use the last position > and coordinates even though one mentions > gen_vel as yes in .mdp file? > > Sincerely, > > Prabir > > On Thu, Sep 19, 2019 at 12:08 PM Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > If grompp sees that your .mdp file asks for it to generate velocities, it > > does so and reports it in the terminal output. You will see that for your > > NVT grompp and not for your NPT grompp. > > > > You can also use gmx dump -s the.tpr to observe whether the velocities > > match the input you gave to the NPT grompp. > > > > Mark > > > > On Thu, 19 Sep 2019 at 18:58, Prabir Khatua <prabir07c...@gmail.com> > > wrote: > > > > > Hello Gromacs users, > > > > > > I have a confusion about generating tpr file from .gro. I have not used > > -t > > > option while > > > generating .tpr file. Please note that in this case, I first did a > > > simulation in NVT ensemble > > > followed by NPT ensemble. In case of NPT run, I am using gen_vel option > > as > > > no in the mdp file and the last gro file that I used for generating tpr > > for > > > the next run (NVT) had both position and velocities. However, the > output > > of > > > grompp option showed a seed value but I am not sure whether it was same > > as > > > that of the NVT run. So my concern is whether it considered the > > velocities > > > from the .gro file or it generated a new set of velocities. If it > > > generated the new set of velocities, can anyone tell me what was the > job > > of > > > -c option corresponding to .gro file that contained both position and > > > velocities or -c option works for only position? Any help would be > > > appreciated. > > > > > > Thanks in advance! > > > > > > Prabir > > > > > > -- > > > > > > *Prabir Khatua* > > > *Postdoctoral Research Associate* > > > *Department of Chemistry & Biochemistry* > > > *University of Oklahoma* > > > *Norman, Oklahoma 73019* > > > *U. S. A.* > > > -- > > > 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. > > > > > -- > > *Prabir Khatua* > *Postdoctoral Research Associate* > *Department of Chemistry & Biochemistry* > *University of Oklahoma* > *Norman, Oklahoma 73019* > *U. S. A.* > -- > 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.