2012/2/10 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@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 <tel:2147483648>. It should
have been within [ 0 .. 27744 ]
Please report this to the mailing list (gmx-users@gromacs.org
<mailto:gmx-users@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 <jalem...@vt.edu <mailto:jalem...@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
vital...@zedat.fu-berlin.de <mailto:vital...@zedat.fu-berlin.de>
francesca.vital...@fu-berlin.de
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Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
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