[gmx-users] Energy minimization Error

Fri Feb 10 14:53:12 CET 2012

On 11/02/2012 12:41 AM, francesca vitalini wrote:
> In order to overcome the problem I tried to fix everything except the 
> backbone (solvent, sidechain and CA, as I want the structure to be 
> maintained). However, if I do then I have problems with the energy 
> minimization as the force on the 15300 is infinite.
>
> Getting Loaded...
> Reading file EM1-1.tpr, VERSION 3.3.1 (single precision)
> Loaded with Money
>
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+01
>    Number of steps    =         2000
> -------------------------------------------------------        inf, 
> atom= 15300
> Program mdrun, VERSION 3.3.1
> Source code file: nsgrid.c, line: 226
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
>
> Variable ci has value -2147483648. It should have been within [ 0 .. 
> 27744 ]
> Please report this to the mailing list (gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>)
> -------------------------------------------------------
>
> "Oh My God ! It's the Funky Shit" (Beastie Boys)
>
> Halting program mdrun
>
> You suggested to check if there is any overlapping.

... so you need to get out some visualization software and look at the 
transformed structure :)

> There might be as my structure is obtained through a reverse 
> transformation from a CG representation. In the mapping the atoms are 
> positioned randomly in the bead. Now I'm running some energy 
> minimization to equilibrate those atoms. I had to solvate the system 
> after the mapping (couldn't do it before due to problems with ions)but 
> I haven't equilibrated it yet and I'm keeping it fixed which could 
> also be a source of overlapping.

Local minimization with EM cannot in general take a "random" positioning 
of the generated atoms and make it one that will be stable under MD. 
Some structure knowledge needs to be build into the reverse transformation.

Mark

> Any ideas?
> Thanks.
> Francesca
>
>
> 2012/2/10 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
>
>
>     francesca vitalini wrote:
>
>         I achieve
>
>         Steepest Descents converged to machine precision in 205 steps,
>         but did not reach the requested Fmax < 10.
>         Potential Energy  = -1.49131940478719e+07
>         Maximum force     =  1.09664530279637e+06 on atom 1520  
>          (parto of the protein)
>         Norm of force     =  2.28369808518165e+06
>
>
>     The magnitude of the force suggests atomic overlap somewhere.
>      Start by investigating the environment around atom 1520.
>
>
>         and the system looked with vmd doesn't look as if it was
>         exploding. However, I have warnings about the table extension
>         and I don't know why but gromacs writes pdb files sometime.
>         However I thought that there
>
>
>     The "step.pdb" files are written when mdrun is about to crash.
>
>
>         might have been an error in the way I defined the position
>         restraints, in fact in the mdp file I hade define = -DEPOSRE
>         while in the topology I had ifdef DEFINE_WAT, so it might have
>         moved it all without fixing the water. So I tried again and
>         this time I got
>
>
>     The "define" statements are literal, so be careful of typos.
>      -DEPOSRE will not work when the topology calls for -DPOSRES.  So
>     unless you've changed default naming for "define" statements,
>     you're not going to get what you expect.
>
>
>         Steepest Descents converged to machine precision in 72 steps,
>         but did not reach the requested Fmax < 10.
>         Potential Energy  = -2.0135496e+07
>         Maximum force     =  2.0486184e+12 on atom 4479
>         Norm of force     =  7.2424045e+13
>
>
>     Again, symptomatic of severe atomic overlap.
>
>
>         but again the same issue with table extent and still the
>         production of pdb files.
>
>         Any explanations?
>
>
>     Investigate the starting configurations near the problematic atoms.
>
>     http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>
>     -Justin
>
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
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>
>
> -- 
> Francesca Vitalini
>
> PhD student at Computational Molecular Biology Group,
> Department of Mathematics and Informatics, FU-Berlin
> Arnimallee 6 14195 Berlin
>
> vitalini at zedat.fu-berlin.de <mailto:vitalini at zedat.fu-berlin.de>
> francesca.vitalini at fu-berlin.de <mailto:francesca.vitalini at fu-berlin.de>
>
> +49 3083875776
> +49 3083875412
>
>
>

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