[gmx-users] simulation continuation without -t option

[Mark Abraham]

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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