Re: high atom velocity

From: francesco oteri (
Date: Tue May 04 2010 - 16:33:43 CDT

I had the same problem and i discovered that depends from compilation
option: if you use standard compilation ooption you shouldn't have any

2010/5/4, Mark M Huntress <>:
> Hi,
> 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.
> Thanks.
> Mark

Cordiali saluti, Dr.Oteri Francesco

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