[gmx-users] simulation continuation without -t option

Mark Abraham mark.j.abraham at gmail.com
Thu Sep 19 19:08:17 CEST 2019


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.


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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