[gmx-users] Energy minimization Error
Mark.Abraham at anu.edu.au
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.
> Any ideas?
> 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.
> 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
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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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