[gmx-users] Energy minimization Error

francesca vitalini francesca.vitalini11 at gmail.com
Fri Feb 10 14:41:12 CET 2012

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=
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)

"Oh My God ! It's the Funky Shit" (Beastie Boys)

Halting program mdrun

You suggested to check if there is any overlapping. 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.
Any ideas?

2012/2/10 Justin A. Lemkul <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<http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System>
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412
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