Subject: Compatibility issue between StreaMD, MDAnalysis, and GROMACS 2026 TPR files

[dsnbkprasanth]

Dear StreaMD Development Team,

Thank you for developing and maintaining StreaMD. We have been using the software extensively for molecular dynamics trajectory analysis and greatly appreciate the automated workflow it provides.

We would like to report a compatibility issue encountered while using StreaMD with recent versions of GROMACS.

System details:

Operating System: Ubuntu Linux
GPU: NVIDIA GeForce RTX 5070
GROMACS version: 2026.x
StreaMD version: Latest available release
MDAnalysis version bundled with StreaMD: (please specify if known)

Issue:

StreaMD fails to process trajectories generated with GROMACS 2026 because it is unable to read the .tpr file generated by this version. The error indicates that the TPR format version is unsupported.

Example error:

Unsupported TPR version 138

The same trajectory can be analyzed successfully using standalone MDAnalysis scripts after upgrading to the latest MDAnalysis release. However, StreaMD appears to rely on an older MDAnalysis version that does not yet support GROMACS 2026 TPR files.

Since newer NVIDIA Blackwell GPUs such as the RTX 5070 require recent GROMACS releases (2025/2026) for optimal performance, support for newer TPR formats would be highly beneficial for users adopting modern hardware.

Could you please consider:

Updating the MDAnalysis dependency bundled with StreaMD.
Adding support for GROMACS 2026 TPR files (TPR version 138).
Providing guidance regarding the currently recommended GROMACS version for StreaMD compatibility.

StreaMD is an excellent platform for automated MD analysis, and support for recent GROMACS versions would significantly improve its usability for the community.

Thank you for your time and for your continued development efforts.

[avnikonenko]

Thank you for reporting this issue!

I fully agree that supporting the latest versions is important. I will make sure to fix this as soon as possible, and I expect it will be ready to use next week.

[dsnbkprasanth]

Dear Anvikoenko,
Has the update been completed by your team? Please let me know.
Thank you.

[avnikonenko]

Hello,
I have updated the MDAnalysis dependency, so StreaMD should now support TPR files generated by GROMACS 2026, including TPR version 138, however If any problem occurs, please, let me know.
For now, the default StreaMD environment still uses GROMACS 2025.2 intentionally, mainly to preserve compatibility with gmx_MMPBSA, which is part of the full StreaMD workflow.

To use new version - please remove the old streamd environment and reinstall env/env_gpu.yml + the latest from git streamd package.

If there is interest, I can add a separate environment file with the latest python GROMACS version, independent of gmx_MMPBSA compatibility.

Best,
Aleksandra

[dsnbkprasanth]

Dear Aleksandra, Please make separate environment file with the latest python GROMACS version, independent of gmx_MMPBSA compatibility. Error: Program: gmx mdrun, version 2025.2-conda_forge Source file: src/gromacs/gpu_utils/cudautils.cuh (line 281) Function: launchGpuKernel<gmx::NBAtomDataGpu, gmx::NBParamGpu, gmx::GpuPairlist, int>(void (*)(gmx::NBAtomDataGpu, gmx::NBParamGpu, gmx::GpuPairlist, int), const KernelLaunchConfig&, const DeviceStream&, CommandEvent*, const char*, const std::array<void*, 4>&)::<lambda()> Assertion failed: Condition: stat == cudaSuccess GPU kernel (k_pruneonly) failed to launch: CUDA error #218 (cudaErrorInvalidPtx): a PTX JIT compilation failed. For more information and tips for troubleshooting, please check the GROMACS website at https://manual.gromacs.org/current/user-guide/run-time-errors.html ------------------------------------------------------- *Failed to run command at line 18 of /media/balu/18EA6F7DEA6F5652/streamd-master/streamd/scripts/script_sh/equlibration.sh* (streamd) ***@***.***:/media/balu/18EA6F7DEA6F5652/Sundeep_Project/DNP/md_files/md_run/4ey7_DNP_4ey7_h_out01_model_1_replica1$ cat /media/balu/18EA6F7DEA6F5652/Sundeep_Project/DNP/md_files/md_run/4ey7_DNP_4ey7_h_out01_model_1_replica1/streamd_bash____08-07-2026-22-16-46.log Script running:***************************** Analysis of MD simulation ********************************* :-) GROMACS - gmx trjconv, 2025.2-conda_forge (-: Executable: /home/balu/miniconda3/envs/streamd/bin.AVX2_256/gmx Data prefix: /home/balu/miniconda3/envs/streamd Working dir: /media/balu/18EA6F7DEA6F5652/Sundeep_Project/DNP/md_files/md_run/4ey7_DNP_4ey7_h_out01_model_1_replica1 Command line: gmx trjconv -s /media/balu/18EA6F7DEA6F5652/Sundeep_Project/DNP/md_files/md_run/4ey7_DNP_4ey7_h_out01_model_1_replica1/md_out.tpr -f /media/balu/18EA6F7DEA6F5652/Sundeep_Project/DNP/md_files/md_run/4ey7_DNP_4ey7_h_out01_model_1_replica1/md_out.xtc -pbc nojump -o md_out_noj_noPBC.xtc Will write xtc: Compressed trajectory (portable xdr format): xtc Reading file /media/balu/18EA6F7DEA6F5652/Sundeep_Project/DNP/md_files/md_run/4ey7_DNP_4ey7_h_out01_model_1_replica1/md_out.tpr, VERSION 2026.1 (single precision)

…

------------------------------------------------------- Program: gmx trjconv, version 2025.2-conda_forge Source file: src/gromacs/fileio/tpxio.cpp (line 2996) Fatal error: reading tpx file *(/media/balu/18EA6F7DEA6F5652/Sundeep_Project/DNP/md_files/md_run/4ey7_DNP_4ey7_h_out01_model_1_replica1/md_out.tpr)version 138 with version 137 program* For more information and tips for troubleshooting, please check the GROMACS website at https://manual.gromacs.org/current/user-guide/run-time-errors.html ------------------------------------------------------- Note that major changes are planned in future for trjconv, to improve usability and utility. Failed to run command at line 7 of /media/balu/18EA6F7DEA6F5652/streamd-master/streamd/scripts/script_sh/md_analysis.sh With Regards, *Dr. D. S. N. B. K. Prasanth., M. Pharm., Ph.D.,* Assistant Professor, School of Pharmacy and Technology Management (SPTM), SVKM's NMIMS Deemed to Be University, Plot no.B4, Green Industrial Park, Polepally SEZ, TSIIC, Jadcherla, Mahbubnagar, Telangana 509 301 Ph: +91-7382027437, email: ***@***.*** ***@***.*** Scopus ID: Prasanth, Dsnbk Sree Naga Bala Krishna - Author details - Scopus <https://www.scopus.com/authid/detail.uri?authorId=56641599900> To know about my previous research and publications you can find more information here in the following links https://orcid.org/0000-0001-5028-1283

On Wed, Jul 8, 2026 at 4:42 PM Aleksandra ***@***.***> wrote: *avnikonenko* left a comment (ci-lab-cz/streamd#85) <#85 (comment)> Hello, I have updated the MDAnalysis dependency, so StreaMD should now support TPR files generated by GROMACS 2026, including TPR version 138, however If any problem occurs, please, let me know. For now, the default StreaMD environment still uses GROMACS 2025.2 intentionally, mainly to preserve compatibility with gmx_MMPBSA, which is part of the full StreaMD workflow. To use new version - please remove the old streamd environment and reinstall env/env_gpu.yml + the latest from git streamd package. If there is interest, I can add a separate environment file with the latest python GROMACS version, independent of gmx_MMPBSA compatibility. Best, Aleksandra — Reply to this email directly, view it on GitHub <#85?email_source=notifications&email_token=AX6ARENVOMORK5EQVVM3DS35DYUBVA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIOJRGQYTQNJVHEYKM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L#issuecomment-4914185590>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AX6ARELME6UT6RHCXWCO4CT5DYUBVAVCNFSNUABFKJSXA33TNF2G64TZHM2DMMRXGA3TAMBVHNEXG43VMU5TIOBQGA4TGOJVGQ4KC5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AX6AREJINEKMP3KJ65IZNH35DYUBVA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIOJRGQYTQNJVHEYKM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/AX6AREJMDAWIK324Z4IJ74L5DYUBVA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIOJRGQYTQNJVHEYKM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you authored the thread.Message ID: ***@***.***>

[avnikonenko]

I tested the GROMACS 2026 environment. The simulation itself runs correctly, so the blocker is not GROMACS execution but the analysis step.
MDAnalysis currently fails to read the GROMACS 2026 .tpr file with:
Your tpx version is 138, which this parser does not support

I could not find a newer stable MDAnalysis release on PyPI/conda-forge that supports this TPR/TPX version. The practical temporary workaround would be to fall back to .gro files when .tpr parsing fails. This should be sufficient for basic analyses such as RMSD/RMSF, but it is not reliable for ProLIF because ProLIF requires proper molecular topology information.

So I can add a .gro fallback for basic analysis, but ProLIF should remain unsupported for GROMACS 2026 outputs until MDAnalysis adds support for TPX version 138.

[avnikonenko]

env_gromacs2026.yml
env_gromacs2026_gpu.yml
Here are tested enviroment files for gromacs 2026 support. No prolif or gbsa analysis is supported yet.

[dsnbkprasanth]

Hello Ci-Lab-Cz/Streamd Team, Did the latest version of MDAnalysis, which supports TPR 138, integrate with streamd? Please let me know. I want to explore further. Thank you. With Regards, *Dr. D. S. N. B. K. Prasanth., M. Pharm., Ph.D.,*

[avnikonenko]

Hello!
TPR 138 support (GROMACS 2026.0) was added in MDAnalysis to develop. It is not in a tagged release yet and until 2.11.0 ships you can install MDAnalysis from develop into the StreaMD environment.
I tested this against our pinned stack and StreaMD runs fine with it. Please use environment files shared above:
#85 (comment)

# create the StreaMD environment as usual
wget https://github.com/user-attachments/files/29818204/env_gromacs2026.yml
or
wget https://github.com/user-attachments/files/29818167/env_gromacs2026_gpu.yml

mamba env create -f env_gromacs2026.yml -n md_tpr138     # or env_gromacs2026_gpu.yml for the CUDA 
mamba activate md_tpr138
pip install git+https://github.com/ci-lab-cz/streamd.git
# replace MDAnalysis with the development version that reads TPR 138
pip install "git+https://github.com/MDAnalysis/mdanalysis@develop#subdirectory=package"

Verify:

python -c "import MDAnalysis as mda; from MDAnalysis.topology.tpr import setting as s; \
print(mda.__version__, 138 in s.SUPPORTED_VERSIONS)"
# -> 2.11.0-dev0 True

One caveat: 2.11.0-dev0 is a pre-release snapshot, so I can't pin it in env.yml —
this is a workaround for users who already have GROMACS 2026 files, not the supported
default. I'll bump the pin as soon as MDAnalysis 2.11.0 is tagged, and then the extra
step goes away. Leaving this issue open to track that.

Please let me know if anything misbehaves.

Best regards,
Aleksandra

[dsnbkprasanth]

Dear Aleksandra, Can you help me with the errors that I always associate with? Please find the attachment. With Regards, *Dr. D. S. N. B. K. Prasanth., M. Pharm., Ph.D.,* Assistant Professor, School of Pharmacy and Technology Management (SPTM), SVKM's NMIMS Deemed to Be University, Plot no.B4, Green Industrial Park, Polepally SEZ, TSIIC, Jadcherla, Mahbubnagar, Telangana 509 301 Ph: +91-7382027437, email: ***@***.*** ***@***.*** Scopus ID: Prasanth, Dsnbk Sree Naga Bala Krishna - Author details - Scopus <https://www.scopus.com/authid/detail.uri?authorId=56641599900> To know about my previous research and publications you can find more information here in the following links https://orcid.org/0000-0001-5028-1283

…

On Thu, Aug 13, 2026 at 3:20 AM Aleksandra ***@***.***> wrote: *avnikonenko* left a comment (ci-lab-cz/streamd#85) <#85 (comment)> Hello! TPR 138 support (GROMACS 2026.0) was added in MDAnalysis to develop. It is not in a tagged release yet and until 2.11.0 ships you can install MDAnalysis from develop into the StreaMD environment. I tested this against our pinned stack and StreaMD runs fine with it. Please use environment files shared above: #85 (comment) <#85 (comment)> # create the StreaMD environment as usual wget https://github.com/user-attachments/files/29818204/env_gromacs2026.yml or wget https://github.com/user-attachments/files/29818167/env_gromacs2026_gpu.yml mamba env create -f env_gromacs2026.yml -n md_tpr138 # or env_gromacs2026_gpu.yml for the CUDA mamba activate md_tpr138 pip install git+https://github.com/ci-lab-cz/streamd.git# replace MDAnalysis with the development version that reads TPR 138 pip install ***@***.***#subdirectory=package" Verify: python -c "import MDAnalysis as mda; from MDAnalysis.topology.tpr import setting as s; \print(mda.__version__, 138 in s.SUPPORTED_VERSIONS)"# -> 2.11.0-dev0 True One caveat: 2.11.0-dev0 is a pre-release snapshot, so we can't pin it in env.yml — this is a workaround for users who already have GROMACS 2026 files, not the supported default. We'll bump the pin as soon as MDAnalysis 2.11.0 is tagged, and then the extra step goes away. Leaving this issue open to track that. Please let me know if anything misbehaves. — Reply to this email directly, view it on GitHub <#85?email_source=notifications&email_token=AX6AREL5567JXEEYTNF6BPT5JTRB7A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRXGMYTSMJWHEZKM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L#issuecomment-5273191692>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AX6AREJTSZL2GX2GWGLZ2XT5JTRB7AVCNFSNUABFKJSXA33TNF2G64TZHM2DMMRXGA3TAMBVHNEXG43VMU5TIOBQGA4TGOJVGQ4KC5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AX6AREMNW4BDZW4Z2IPQZGT5JTRB7A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRXGMYTSMJWHEZKM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/AX6AREK3OKXUIT7PY2DQ33L5JTRB7A5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRXGMYTSMJWHEZKM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you authored the thread.Message ID: ***@***.***>

[avnikonenko]

I can't find the attachment. Could you please re-attach it here again?