From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Wed Sep 29 2021 - 15:36:27 CDT
Do you use margin?
Say "margin 3" in your input file?
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:shekaari_at_email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.google.com/citations?hl=en&user=LDzbXB4AAAAJ&view_op=list_works&sortby=pubdate__;!!DZ3fjg!vrLeITbBWwmIzRJivX7pxWVf9-AWwnBUHAMx56eZ1SMBwFfJNtbWE5AnLnLEj-0D2w$ ]
From: "Hasith Sathsindu" <hasith.sathsindu_at_gmail.com>
To: "namd-l" <namd-l_at_ks.uiuc.edu>
Sent: Wednesday, September 29, 2021 9:53:57 PM
Subject: namd-l: ERROR: Atoms moving too fast; simulation has become unstable.
I am dealing with the type III collagen (single) molecule in a water box. I need to apply a constant force to all the carbon atoms except carbon atoms of last residue which are fixed.
But that causes an error.
ERROR: Atom 343 velocity is 8090.26 -7576.1 3976.9 (limit is 6000)
ERROR: Atoms moving too fast; simulation has become unstable.
I used tip4 water molecules to the water box. Is that possible to do a Non equilibrium simulation to this structure?
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