[gmx-users] Batch mode error in GROMACS version 2019.2

[Rajib Biswas]

Hi David,

As I said in my previous email, when I am using

echo 18 0 | gmx_mpi energy -f traj.edr -o temperature

getting the following error:

Program:     gmx energy, version 2019.2
Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296)

Fatal error:
No energy terms selected


However, if I use

echo 18 0 | gmx_d energy -f traj.edr -o temperature

There is no error.
Note that for both the cases (i.e. gmx_mpi and gmx_d) interactive mode is
working fine.


Thanks.

With regards,
Rajib


On Sat, Sep 14, 2019 at 12:56 PM David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> Den 2019-09-14 kl. 08:36, skrev Rajib Biswas:
> > I did some more experimentation about this and found that this error is
> > coming only with the mpi enabled version.
> please give the exact command line
> >
> > Rajib
> >
> > On Fri, Sep 13, 2019 at 10:58 PM Rajib Biswas <chemrajib at gmail.com>
> wrote:
> >
> >> Hi Mark,
> >>
> >> Thanks!
> >>
> >> Interactively I could do it without any error. However, this error only
> >> arises whenever I have tried to use batch mode.
> >>
> >> With regards,
> >> *Rajib*
> >>
> >>
> >> On Fri, Sep 13, 2019 at 6:06 PM Mark Abraham <mark.j.abraham at gmail.com>
> >> wrote:
> >>
> >>> What happens when you do it interactively?
> >>>
> >>> Mark
> >>>
> >>> On Fri, 13 Sep 2019 at 14:21, Rajib Biswas <chemrajib at gmail.com>
> wrote:
> >>>
> >>>> Dear All,
> >>>>
> >>>> I am trying to use the post-processing tools in batch mode. I am using
> >>> the
> >>>> following commands
> >>>>
> >>>> echo 18 0 | gmx_mpi energy -f traj.edr -o temperature
> >>>>
> >>>> Getting the following error:
> >>>>
> >>>> Program:     gmx energy, version 2019.2
> >>>> Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296)
> >>>>
> >>>> Fatal error:
> >>>> No energy terms selected
> >>>>
> >>>>
> >>>> I have even tried all the options mentioned
> >>>>
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
> >>>> however, could not get it worked for version 2019.2.
> >>>>
> >>>> Any help will be appreciated.
> >>>>
> >>>> With regards,
> >>>> *Rajib*
> >>>> --
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>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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