[gmx-users] simulation continuation without -t option

[Prabir Khatua]

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.abraham at 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 <prabir07chem at 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-request at 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-request at gromacs.org.
>


-- 

*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*