Issues running csg_inverse in the tutorials.

[ARTHUR LIN]

Hi everybody,

I installed VOTCA with conda on an HPC cluster, and I am running through the VOTCA tutorials. I am trying to run csg_inverse for IBI for the SPCE water system with the GROMACS within the VOTCA conda package. I keep obtaining the following error: 

Fatal error: The group cutoff scheme has been removed since GROMACS 2020. Please use the Verlet cutoff scheme.

I've attached the full inverse.log file. This GROMCAS version is the one that came packaged with conda (as shown in the attached inverse.log), but I also tried linking this to a version of GROMACS I built with the -DGMX_INSTALL_LEGACY_API=ON option in cmake, but I get the same error message. 

• The linking was done by including the following xml in the settings.xml:
  
        <grompp>
  <bin>/software/alin62/gromacs-2024.5_mpi/bin/gmx grompp
  <DESC> Name (or absolute path) of the grompp binary</DESC>
  </bin>
  <opts>
  <DESC> Additional options to Gromacs grompp (e.g. -maxwarn 1)</DESC>
  </opts>
  </grompp>

The same fatal error appears with csg_inverse for the spce relative entropy tutorial as well, for what I believe to be similar reasons.

Any help would be much appreciated -- for now I will try using LAMMPS to complete the tutorial.

Sincerely,

Arthur.

[Christoph Junghans]

On Sat, Jan 25, 2025 at 7:09 AM 'ARTHUR LIN' via votca
<vo...@googlegroups.com> wrote:
>
> Hi everybody,
>
> I installed VOTCA with conda on an HPC cluster, and I am running through the VOTCA tutorials. I am trying to run csg_inverse for IBI for the SPCE water system with the GROMACS within the VOTCA conda package. I keep obtaining the following error:
>
> Fatal error: The group cutoff scheme has been removed since GROMACS 2020. Please use the Verlet cutoff scheme.

The error just means your gromacs is too new. Tabulated interactions
are only supported in gromacs up to version 2019.
See https://gitlab.com/gromacs/gromacs/-/issues/1347

Christoph

>
> I've attached the full inverse.log file. This GROMCAS version is the one that came packaged with conda (as shown in the attached inverse.log), but I also tried linking this to a version of GROMACS I built with the -DGMX_INSTALL_LEGACY_API=ON option in cmake, but I get the same error message.
>
> The linking was done by including the following xml in the settings.xml:
> <grompp>
> <bin>/software/alin62/gromacs-2024.5_mpi/bin/gmx grompp
> <DESC> Name (or absolute path) of the grompp binary</DESC>
> </bin>
> <opts>
> <DESC> Additional options to Gromacs grompp (e.g. -maxwarn 1)</DESC>
> </opts>
> </grompp>
>
>
> The same fatal error appears with csg_inverse for the spce relative entropy tutorial as well, for what I believe to be similar reasons.
>
> Any help would be much appreciated -- for now I will try using LAMMPS to complete the tutorial.
>
> Sincerely,
> Arthur.
>

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--
Christoph Junghans
Web: http://www.compphys.de

[ARTHUR LIN]

Hi Christoph,

Thank you for the reply -- I thought that compiling with the flag -DGMX_INSTALL_LEGACY_API=ON would enable me to use older features but alas. 

I tried installing GROMACS 2019 on the HPC, with the intention to link it to the VOTCA scripts but was running into installation issues, so that didn't work.

Do you think it's worth raising an issue on Github to provide GROMACS 2019 within the VOTCA conda package so that things work more out of the box? Currently, GROMACS 2024 is being packaged together with VOTCA, so tabulated interactions aren't working. 

Sincerely,

Arthur

[Christoph Junghans]

Christoph Junghans

Web: http://www.compphys.de

On Sat, Jan 25, 2025 at 12:01 'ARTHUR LIN' via votca <vo...@googlegroups.com> wrote:

Hi Christoph,

Thank you for the reply -- I thought that compiling with the flag -DGMX_INSTALL_LEGACY_API=ON would enable me to use older features but alas.

That only enables the old API that we use to read gromacs files, but not old features like tabulated interactions.

I tried installing GROMACS 2019 on the HPC, with the intention to link it to the VOTCA scripts but was running into installation issues, so that didn't work.

Yeah, gromacs upstream still supports 2019, but it gets harder and harder to build. We also have to patch things in our container.

Do you think it's worth raising an issue on Github to provide GROMACS 2019 within the VOTCA conda package so that things work more out of the box? Currently, GROMACS 2024 is being packaged together with VOTCA, so tabulated interactions aren't working. 

Yes, I think it would be worth asking the conda guys to package gromacs 2019 and to comment on the gromacs issue below so tabulated interactions get rereimplemented in newer versions of gromacs.

Christoph

To view this discussion visit https://groups.google.com/d/msgid/votca/24b8edd5-50d6-4720-853d-693889653f91n%40googlegroups.com.

[ARTHUR LIN]

Thanks, Christoph! I will raise these issues.