NAMD can not run 5.6 million system with amber prmtop

From: Chunli Yan (utchunliyan_at_gmail.com)
Date: Fri Nov 04 2022 - 12:44:22 CDT

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Hello,

I have a protein-DNA system with a total atom number ~5.6 million. After we
generated the amber prmtop files, we can not use VMD to visualize them (in
vmd: PARM7: error reading bond number 3995983) and also can not run with
NAMD.

I am wondering whether the system is too big and can not run (we do not
have issues for smaller systems with amber prmtop), whether charmm psf will
work for larger systems.

Best,

*Chunli*

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