[gmx-users] simulation continuation without -t option

[Prabir Khatua]

Thanks a lot Mark!

Prabir

On Thu, Sep 19, 2019 at 9:50 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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, <prabir07chem at 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.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.*
> > > > --
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> > --
> >
> > *Prabir Khatua*
> > *Postdoctoral Research Associate*
> > *Department of Chemistry & Biochemistry*
> > *University of Oklahoma*
> > *Norman, Oklahoma 73019*
> > *U. S. A.*
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-- 

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