# One system not plateauing in NPT before SMD comparison across multiple complexes

**URL:** <https://gromacs.bioexcel.eu/t/one-system-not-plateauing-in-npt-before-smd-comparison-across-multiple-complexes/13419>\
**Category:** User discussions\
**Tags:** simulation-setup\
**Created:** [April 28, 2026, 3:19am UTC](https://gromacs.bioexcel.eu/t/one-system-not-plateauing-in-npt-before-smd-comparison-across-multiple-complexes/13419 "2026-04-28T03:19:13Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![rachana](https://avatars.discourse-cdn.com/v4/letter/r/4da419/32.png) [@rachana](https://gromacs.bioexcel.eu/u/rachana)\
**Post date:** [April 28, 2026, 3:19am UTC](https://gromacs.bioexcel.eu/t/one-system-not-plateauing-in-npt-before-smd-comparison-across-multiple-complexes/13419/1 "2026-04-28T03:19:13Z")

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GROMACS version: gromacs/2025.3-openmpi-5.0.8-single-rocky8  
GROMACS modification: Yes/No  
Here post your question

I am comparing **4 TCR–pMHC complexes** using constant-velocity SMD and want to compare rupture force, peak force, and work.

The 3 systems look stable after 500 ps final NPT, but 1 system still shows slow backbone RMSD drift.

Is it acceptable to extend only that system to 1 ns before SMD?

Or should all systems use exactly the same equilibration length for a fair comparison?

Temperature, pressure, and density are stable for this system.

I am new to molecular dynamics and SMD, so I am a bit unsure how to proceed in this situation and would really appreciate guidance on the best practice here.

 ![Backbone RMSD_NPT4_equilibration-TCR6.1_plot](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/128b3d5d59bc54c7a6ca17f2c2af6465c6b8ffaf.png)