[gmx-users] Energy minimization Error

Fri Feb 10 16:48:00 CET 2012

In fact in the reverse transformation I'm feeding the CG structure
information.
Once I look through VMD to the FG structure I notice that the backbones are
not in planes so definitely I need to run some minimization there. In the
tutorial they were using simulating annealing, but I don't think I need
more than energy minimization for that.
What do you think?

2012/2/10 Mark Abraham <Mark.Abraham at anu.edu.au>

>  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)
> -------------------------------------------------------
>
> "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>
>
>>
>>
>> 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 | (540) 231-9080
>> 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
> francesca.vitalini at fu-berlin.de
>
> +49 3083875776
> +49 3083875412
>
>
>
>
>
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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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