run_gromacs.sh: grompp binary 'grompp' not found

[avinesh ojha]

Hi Christoph,

I have been getting this error message-"run_gromacs.sh: grompp binary 'grompp' not found:. I installed Gromacs 2019 with VOTCA 2024.2 when running IBI tutorial example. Can you please help me on this issue? Thanks.

Best,

Avinesh

[Christoph Junghans]

Christoph Junghans

Web: http://www.compphys.de

On Thu, May 15, 2025, 08:09 avinesh ojha <ojha.a...@gmail.com> wrote:

Hi Christoph,

I have been getting this error message-"run_gromacs.sh: grompp binary 'grompp' not found:. I installed Gromacs 2019 with VOTCA 2024.2 when running IBI tutorial example. Can you please help me on this issue? Thanks.

It should be calling "gmx grompp", did you set to grompp manually in your settings file?

Christoph

Best,

Avinesh

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[avinesh ojha]

Sorry didnt quite get it. I didn't change/set anything in the settings.xml file from the tutorial.  Thanks. 

Best,

Avinesh

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[Christoph Junghans]

On Thu, May 15, 2025 at 9:30 AM avinesh ojha <ojha.a...@gmail.com> wrote:
>
> Sorry didnt quite get it. I didn't change/set anything in the settings.xml file from the tutorial. Thanks.

Ok, can you post your inverse.log and the csg_defaults.xml from your
installation?

Thanks,

Christoph

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[avinesh ojha]

Hi Christoph,

Attached are the files-inverse.log and csg_defaults.xml. I noticed that csg_defaults did not exist under xml folder. So I just copied the one I am sharing with you. Thank you.

Best,

Avinesh

[Christoph Junghans]

Your log file says:

-------------------------------
Incomplete step 1
WARNING: options file ('/my_files/ibi_gromacs-multi/settings.xml') was changed since the last execution, these changes will have no effect already finished parts of the iteration, to take effect remove the current iteration ('step_001')

So I would remove step_001 and try again.

Also for the “multi”plexed example (ibi_gromacs-multi) you will need an mpi parallel version of gromacs.

Christoph

Christoph Junghans

Web: http://www.compphys.de

On Tue, May 20, 2025 at 08:59 avinesh ojha <ojha.a...@gmail.com> wrote:

Hi Christoph,

Attached are the files-inverse.log and csg_defaults.xml. I noticed that csg_defaults did not exist under xml folder. So I just copied the one I am sharing with you. Thank you.

Best,

Avinesh

On Thu, May 15, 2025 at 10:09 AM avinesh ojha <ojha.a...@gmail.com> wrote:

Hi Christoph,

I have been getting this error message-"run_gromacs.sh: grompp binary 'grompp' not found:. I installed Gromacs 2019 with VOTCA 2024.2 when running IBI tutorial example. Can you please help me on this issue? Thanks.

Best,

Avinesh

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[avinesh ojha]

Hi Christoph,

I did try on ibi tutorial also, and have the same issue even when I remove step_001.  Thank you.

Best,

Avinesh Ojha, PhD

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[Christoph Junghans]

Christoph Junghans

Web: http://www.compphys.de

On Tue, May 20, 2025 at 09:58 avinesh ojha <ojha.a...@gmail.com> wrote:

Hi Christoph,

I did try on ibi tutorial also, and have the same issue even when I remove step_001.  Thank you.

can you call csg_inverse with the extra option “clean”, then start over and see if it still fails. If so post your new inverse.log

Christoph

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[avinesh ojha]

I used the option clean and attached is the inverse file after I rerun. 

Best,

Avinesh 

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[Christoph Junghans]

Christoph Junghans

Web: http://www.compphys.de

On Tue, May 20, 2025 at 10:49 avinesh ojha <ojha.a...@gmail.com> wrote:

I used the option clean and attached is the inverse file after I rerun. 

Your log file indicates you are using votca 1.2.4 which is rather old.

Can you confirm by running “csg_inverse --version”?

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[avinesh ojha]

Yes, I checked csg_property and it shows version 1.2.4 (Compiled Jan 3 2016). 

Just to let you know, when I run "csg_inverse --version", it outputs an error saying unknown option '--version'. 

Is it the version issue? I can install a new one if thats the case. Thank you.

Best,

Avinesh

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[Christoph Junghans]

Christoph Junghans

Web: http://www.compphys.de

On Wed, May 21, 2025 at 03:36 avinesh ojha <ojha.a...@gmail.com> wrote:

Yes, I checked csg_property and it shows version 1.2.4 (Compiled Jan 3 2016). 

Just to let you know, when I run "csg_inverse --version", it outputs an error saying unknown option '--version'. 

Is it the version issue? I can install a new one if thats the case. Thank you.

yes, votca v1.2.4 was released more than 10 years ago, we cannot support a version that old anymore, so please update.

Christoph

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