Protein ns MD simulation and other times recommended inquiry?

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1

GROMACS version:
GROMACS modification: Yes/No
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Hello I simulated a heptamer transmembrane protein 426-residues per chain (2982 residues total), using the methodology and indicated times (eg. 1-ns MD simulation) from Tutorial One: Lysozyme in Water. Would a recommendation of using 100-ns and any other time increases within this tutorial be warranted in this case towards confirming satisfactory RMSD etc. Analysis or considering the above the tutorial may be followed as is? Thanks if you know:), Joel

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Refer to published studies of similarly sized systems for guidance, but large systems like you’re describing, including a membrane, often require hundreds of ns to even equilibrate before running data collection. RMSD doesn’t tell you anything about the adequacy of equilibration or sampling.

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Hi Justin ok thank you for your kind and prompt update:) will do.