NAMD can not run 5.6 million system with amber prmtop

From: Chunli Yan (
Date: Fri Nov 04 2022 - 12:44:22 CDT


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

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.



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