From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Nov 05 2003 - 17:36:51 CST
Hello,
Just thinking outloud...
It is not common to equilibrate a protein without some sort of solvation
unless you mean you are minimizing the protein, but that would not
generate the error you see.
You didn't answer the question about how you are heating the protein or
what temperature you are trying to equilibrate to. Again it is strange
that there is no solvent in your equilibration.
Remember that the atom numbers in namd need to have one subtracted from
them to see the same atom in VMD. Are the atoms in question internal or
on the surface of the protein?
Again, with out some kind of idea what temperatures you are at and what
dielectric screening you are using, you could be getting some rather weird
charge interactions..
Brian
On Thu, 6 Nov 2003, himanshu chandola wrote:
> 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 **
> > *****************************************************************
> >
> >
> >
>
-- ***************************************************************** **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 ** *****************************************************************
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