Re: atoms moving too fast

From: himanshu chandola (beu99419_at_ccsun50.iitd.ernet.in)
Date: Thu Nov 06 2003 - 03:59:10 CST

hi,
  i am using a time step of 1fs. I am not solvating my protein - that's
the particular reason i didn't use a box. Increasing the cutoff just made
the 'global exclusion error' which was coming alongwith vanish but still
namd crashes after some odd 199 or some timesteps with the message: atoms
moving too fast. I also looked into the atoms which were cited as moving
fast and there wasn't anything peculiar in them.

Could it be that there is some 'wrong' generation done of my psf and pdb
files - but then the structures are similar and there is no error at the
first time step itself.

----------------------------------------
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.

On Wed, 5 Nov 2003, Brian Bennion wrote:

> 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.
> >
>
> --
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 422-6605 **
> *****************************************************************
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:17:53 CST