From: Bunzeki Kilolo (Mme) (kilolo.bunzeki_at_polytechnique.edu)
Date: Fri Nov 04 2022 - 12:57:17 CDT
Dear Chunli,
I suggest you to create a smaller system around the interaction site that you want to study.
Best,
Kilolo
De: "Chunli Yan" <utchunliyan_at_gmail.com>
À: "NAMD list" <namd-l_at_ks.uiuc.edu>
Envoyé: Vendredi 4 Novembre 2022 18:44:22
Objet: namd-l: NAMD can not run 5.6 million system with amber prmtop
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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