Adjust plain MD simulation PDB writing & production step counter#1302

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IAlibay wants to merge 8 commits intomainfrom

Commits on May 26, 2025

Add final frame to XTC file + write final frame to PDB
IAlibay
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Commits on May 27, 2025

Test something
IAlibay
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Commits on May 29, 2025

Merge branch 'main' into finalframe_xtc
IAlibay
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