Re: high atom velocity

From: francesco oteri (francesco.oteri_at_gmail.com)
Date: Wed May 05 2010 - 14:12:49 CDT

I used intel compiler and i discovered that it doesn't generate the problem

2010/5/4 Mark M Huntress <markmh_at_bgsu.edu>

> Fransesco,
> I am using it on a public cluster, i don't think I can recompile it. What
> did you have to do exactly?
> Thanks, Mark
> ________________________________________
> From: francesco oteri [francesco.oteri_at_gmail.com]
> Sent: Tuesday, May 04, 2010 5:33 PM
> To: Mark M Huntress
> Cc: NAMD
> Subject: Re: namd-l: high atom velocity
>
> I had the same problem and i discovered that depends from compilation
> option: if you use standard compilation ooption you shouldn't have any
> problem
>
> 2010/5/4, Mark M Huntress <markmh_at_bgsu.edu>:
> > 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
>

-- 
Cordiali saluti, Dr.Oteri Francesco

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