GROMACS version: gromacs/2025.3-openmpi-5.0.8-single-rocky8
GROMACS modification: Yes/No
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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.
