Re: How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely

From: Chris Harrison (charris5_at_nd.edu)
Date: Sun Jan 04 2009 - 12:03:37 CST

Sunita,

Repeat the very end of the simulation (starting from a recent set of restart
files), but set your log and dcd updates to 1 to grab every step. Run it
until you get the velocity exceptions again. Load the system into VMD and
find the atoms that are "moving too fast" via:

set sel [atomselect top "serial 3430"]
$sel get resid
$sel get resname
$sel get index
....etc

Make a representation showing that atomselection and "watch it" as you
scroll frame-by-frame through the dcd.

This usually reveals the nature of the underlying problem in pathological
systems.

Alternatively, you may be able to "guess" what is the problem by examining
the energy outputs. What type of energy is the highest. What atomic
interactions are present with the first atom to experience a velocity
exception that are consistent with the type of energy that is highest
(usually orders of magnitude greater than the other energies). Finally,
also look at the size of your system (if running a non-NVT simulation) to
see if you possibly have a barostat problem or alternately examine the
pressure and density of the system.

Best,
C.

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Fri, Jan 2, 2009 at 3:58 AM, sunita gupta <sunita.bio_at_gmail.com> wrote:
> Hi all,
> I am doing the coarse grain simulation of a protein around 600 residues.
> After minimization when I am heating my system I am encountering an error
>
> *"ERROR: Atom 3430 velocity is 3106.47 2328.51 -12.5113 (limit is 1000)
> ERROR: Atom 3548 velocity is 479.695 -98.743 -1895.5 (limit is 1000)
> ERROR: Atom 3782 velocity is -862.237 451.473 -232.745 (limit is 1000)
> ERROR: Atom 3932 velocity is 10558.1 -3567.96 2505.98 (limit is 1000)
> ERROR: Atom 4326 velocity is 2550.07 35.6837 1606.01 (limit is 1000)
> ERROR: Atom 4393 velocity is -74.071 -1839.18 713.27 (limit is 1000)
> ERROR: Atom 4402 velocity is 91.7628 1845.16 -693.08 (limit is 1000)
> ERROR: Atom 5824 velocity is -10546.3 3561.58 -2532.62 (limit is 1000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 7955 velocity is -215.633 -1008.42 -1042.81 (limit is 1000)
> ERROR: Atom 8252 velocity is 396.536 2473.09 152.247 (limit is 1000)
> ERROR: Atom 8345 velocity is 949.577 519.289 -570.563 (limit is 1000)
> ERROR: Atom 8376 velocity is -944.965 -504.078 573.664 (limit is 1000)
> ERROR: Atom 8852 velocity is 71.9893 1061.93 965.823 (limit is 1000)
> ERROR: Atom 8904 velocity is -506.517 109.389 -923.522 (limit is 1000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Exiting prematurely."
> *
> After going through the mailing list I found that its due to not enough
> minimization, so I have minimized it lastly to 20000 steps, but after that
> again I am facing this problem.
> One more thing that I am observing is that the value of GRADIENT TOLERANCE
> is also very high (fluctuating around 40 and never going below 1).
> Can anyone suggest the cure to this problem. Any help will be highly
> appreciated.
>
> Thanks and Regards
> --
> SUNITA GUPTA
>
>
>
>

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