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Support PDBs with more than 100,000 atoms and support ACEMD 4#6

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dkarlov wants to merge 2 commits intomolecularmodelingsection:mainfrom
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Open

Support PDBs with more than 100,000 atoms and support ACEMD 4#6
dkarlov wants to merge 2 commits intomolecularmodelingsection:mainfrom
dkarlov:main