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 -2147483648. It should have been within [ 0 .. 27744 ]<br>Please report this to the mailing list (<a href="mailto:gmx-users@gromacs.org">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. 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>
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">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 class="im"><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 class="im"><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 class="im"><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 class="im">
<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 class="im"><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/<u></u>Documentation/Terminology/<u></u>Blowing_Up#Diagnosing_an_<u></u>Unstable_System</a><span class="HOEnZb"><font color="#888888"><br>
<br>
-Justin</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
-- <br>
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</div></div></blockquote></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><a href="mailto:vitalini@zedat.fu-berlin.de" target="_blank">vitalini@zedat.fu-berlin.de</a><br><a href="mailto:francesca.vitalini@fu-berlin.de" target="_blank">francesca.vitalini@fu-berlin.de</a><br><br>+49 3083875776<br>
+49 3083875412<br><br>