From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Nov 07 2003 - 11:10:34 CST
Hi,
1 GB of memory divided by 24 processes isn't much. Also, you might be
seeing some kind of bug. Let us know if you find something.
-Jim
On Fri, 7 Nov 2003, himanshu chandola wrote:
> hello ,
> the reason for which namd was crashing might be due to the
> architecture of the system - though its a sun box with 24 processors and
> 1gb memory - it had problems with larger processes. I am still cooperating
> with the admin to find out what really happened. So as such the system is
> working fine if i try 6 processes.
>
> I am trying that simulation with 'atoms moving too fast' after having
> done more minimzation steps. Also it appears that in my case it won't
> matter at what temperature i would do the simulation. Hence just to freeze
> the temperature dependent dynamics of the molecules I am now doing the
> simulations at 0K - would communicate if the error reappears.
>
> Thanks everyone again
>
> ----------------------------------------
> 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,
> >
> > 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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