Re: atoms moving too fast

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Nov 05 2003 - 16:50:53 CST

Hello,

What is your timestep? 2.0fs?
Is your protein solvated? What atoms are moving too fast? How fast are you
heating it up? 1 degree every 100 steps?

Increasing your cutoff may or may not make things better. If you don't
have a box for the system you could be accelerating water atoms off into
space at light speed...

On Thu, 6 Nov 2003, himanshu chandola wrote:

> hello everyone,
> I had mailed here earlier about the error about atoms moving
> too fast. I increased my cutoff to 15 just to make sure that errors don't
> appear dude to the reason specified at
> http://www.ks.uiuc.edu/Research/namd/current/ug/node23.html
>
> Still the 'atoms moving too fast' error persists. I also don't have any
> atoms at 'uninitialized --(0,0,0)' coordinates.
>
> My protein is not in a box and at this moment i was just trying to
> equilibrate it.
>
> any suggestions about what could have been possibly gone wrong ?
>
> with kind regards,
>
> himanshu
>
> ----------------------------------------
> Morpheus: Do you believe in fate, Neo?
> Neo: No.
> Morpheus: Why Not?
> Neo: Because I don't like the idea that I'm not in control of my life.
>

-- 
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**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
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