Re: atoms moving too fast

From: himanshu chandola (beu99419_at_ccsun50.iitd.ernet.in)
Date: Thu Nov 06 2003 - 19:11:58 CST

hi,
  well i had my system's initial temperature at 300K and I had langevin
dynamics in place with temperature at 300K. So i didn't heat up my
protein.I didn't solvate my protein because the dynamics simulations which
i intend to do will not be much changed by inclusion of water (which will
increase the computation time). I also did notice the difference between
namd and vmd numbering but the atoms which were moving fast - didn't
suggest something meaningful.

In the meanwhile - i have this second problem with a protein which I am
minimizing over 10000 steps. I get a message and namd exists with the
following message . any clues? and thank you all for being supportive
especially Brian.

LDB: LOAD: AVG 439.251 MAX 703.499 MSGS: TOTAL 48 MAXC 24 MAXP 4 None
LDB: LOAD: AVG 439.251 MAX 527.099 MSGS: TOTAL 80 MAXC 28 MAXP 4 Alg7
LDB: LOAD: AVG 439.251 MAX 448.024 MSGS: TOTAL 81 MAXC 28 MAXP 4 Alg7
Signaled (core dumped).

This occurs after approx 3 minutes into the minimization.

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.

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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