In fact in the reverse transformation I'm feeding the CG structure information. <br>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.<br>
What do you think?<br><br><br><br><div class="gmail_quote">2012/2/10 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div><div class="h5">
On 11/02/2012 12:41 AM, francesca vitalini wrote:
<blockquote type="cite">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.<br>
<br>
Getting Loaded...<br>
Reading file EM1-1.tpr, VERSION 3.3.1 (single precision)<br>
Loaded with Money<br>
<br>
Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+01<br>
Number of steps = 2000<br>
-------------------------------------------------------
inf, atom= 15300<br>
Program mdrun, VERSION 3.3.1<br>
Source code file: nsgrid.c, line: 226<br>
<br>
Range checking error:<br>
Explanation: During neighborsearching, we assign each particle to
a grid<br>
based on its coordinates. If your system contains collisions or
parameter<br>
errors that give particles very high velocities you might end up
with some<br>
coordinates being +-Infinity or NaN (not-a-number). Obviously, we
cannot<br>
put these on a grid, so this is usually where we detect those
errors.<br>
Make sure your system is properly energy-minimized and that the
potential<br>
energy seems reasonable before trying again.<br>
<br>
Variable ci has value -<a href="tel:2147483648" value="+12147483648" target="_blank">2147483648</a>. It should have been within [ 0
.. 27744 ]<br>
Please report this to the mailing list (<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>)<br>
-------------------------------------------------------<br>
<br>
"Oh My God ! It's the Funky Shit" (Beastie Boys)<br>
<br>
Halting program mdrun<br>
<br>
You suggested to check if there is any overlapping.</blockquote>
<br></div></div>
... so you need to get out some visualization software and look at
the transformed structure :)<div class="im"><br>
<br>
<blockquote type="cite"> 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. <br>
</blockquote>
<br></div>
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.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div><div class="h5"><br>
<br>
<blockquote type="cite">
Any ideas?<br>
Thanks.<br>
Francesca<br>
<br>
<br>
<div class="gmail_quote">2012/2/10 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><br>
<br>
francesca vitalini wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I achieve<br>
<br>
Steepest Descents converged to machine precision in 205
steps,<br>
but did not reach the requested Fmax < 10.<br>
Potential Energy = -1.49131940478719e+07<br>
Maximum force = 1.09664530279637e+06 on atom 1520
(parto of the protein)<br>
Norm of force = 2.28369808518165e+06<br>
<br>
</blockquote>
<br>
</div>
The magnitude of the force suggests atomic overlap somewhere.
Start by investigating the environment around atom 1520.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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 <br>
</blockquote>
<br>
</div>
The "step.pdb" files are written when mdrun is about to crash.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<br>
<br>
</blockquote>
<br>
</div>
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.
<div>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Steepest Descents converged to machine precision in 72
steps,<br>
but did not reach the requested Fmax < 10.<br>
Potential Energy = -2.0135496e+07<br>
Maximum force = 2.0486184e+12 on atom 4479<br>
Norm of force = 7.2424045e+13<br>
<br>
</blockquote>
<br>
</div>
Again, symptomatic of severe atomic overlap.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
but again the same issue with table extent and still the
production of pdb files.<br>
<br>
Any explanations?<br>
<br>
</blockquote>
<br>
</div>
Investigate the starting configurations near the problematic
atoms.<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System" target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System</a><span><font color="#888888"><br>
<br>
-Justin</font></span>
<div>
<div><br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</div>
<br>
<br clear="all">
<br>
-- <br>
Francesca Vitalini<br>
<br>
PhD student at Computational Molecular Biology Group, <br>
Department of Mathematics and Informatics, FU-Berlin<br>
Arnimallee 6 14195 Berlin<br>
<br>
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</blockquote>
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PhD student at Computational Molecular Biology Group, <br>Department of Mathematics and Informatics, FU-Berlin<br>Arnimallee 6 14195 Berlin<br><br><a href="mailto:vitalini@zedat.fu-berlin.de" target="_blank">vitalini@zedat.fu-berlin.de</a><br>
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