From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Tue May 04 2010 - 14:36:56 CDT
I have been getting a high atom velocity error a few thousand steps in. It is always a protein hydrogen, but not always the same one. I am equilibrating water solvent and protein hydrogens, keeping heavy atoms fixed.
I have tried everything to fix this, tried everything in the troubleshooting namd webpage, tried expanding the cell basis vectors, tried harmonic constraints instead of fixing, tried more minimization, tried increasing pairlistdist, yet I still get this error. Sometimes the error comes sooner rather than later. Any help would be appreciated, I am really stuck here. If you want to look at files, tell me, it won't let me send the tar.gz package because it is too big.
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