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Moreover,<br>
the problem is not the potential energy, but the force that must
converge.<br>
The "inf" there about force and about atom 1 tells me that the computed
force has problems, indeed.<br>
Which is atom 1 ? Is the protein Nter neutral or charged ? Or is atom 1
an atom from the ligand ?<br>
<br>
Cheers<br>
<br>
L<br>
<br>
<br>
<br>
<blockquote cite="mid:72F15A979E724D109CE549C857093212@AnnaNetbook"
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<div><span class="062391112-21052010"><font face="Arial" size="2">Dear
gmx-users,</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">I
tried to minimize my systems formed by a protein obtained by homology
modelling procedure, in one case with a ligand inside, in the other
case in the apo form.</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">All
worked fine until the minimization step: when I launched mdrun, the
well known "stepsize too small..." communication appears. The program
worked for 37 steps without producing output energies, and the final
report was:</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">Potential
Energy = -6.07e+5 (for the prot+lig); -5.58e+5 (for the protein alone)</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">Maximum
force = inf on atom 1</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">Norm
of force = inf</font></span></div>
<div><span class="062391112-21052010"></span> </div>
<div><span class="062391112-21052010">
<div><font face="Arial"><font size="2"><span
class="062391112-21052010">I had a look to the gmx-user list archive,
but when the "stepsize too small" error is reported, generally the
potential energy is very high. In my case, t</span>he potential energy
seems to be correct (it is negative, and the order of magnitude is
similar to that of other systems I studied before). <span
class="062391112-21052010">U</span>sually when I retrieve this error,
either the potential energy is very positive and high, or there are
errors in the protein, but I visualized the systems with VMD and they
seem to be correct. It would sound VERY strange if I had the
protein already in a minimum of potential energy!!!</font></font> <span
class="062391112-21052010"><font face="Arial" size="2">Moreover, the
same thing happens in both cases, so I don't think it's a problem
related to the ligand.</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">What
do you think about? Could you give me some hint?</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">Thank
you very much and best regards</font></span></div>
<div><span class="062391112-21052010"><font face="Arial" size="2">Anna</font></span></div>
</span></div>
<div><font face="Arial" size="2"><span class="062391112-21052010"></span></font> </div>
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<div align="left"><font face="Arial" size="2">__________________________________________________________________</font></div>
<div align="left"><font face="Arial" size="2">Anna Marabotti, Ph.D.</font></div>
<div align="left"><font face="Arial" size="2">Laboratory of
Bioinformatics and Computational Biology</font></div>
<div align="left"><font face="Arial" size="2">Institute of Food
Science - CNR</font></div>
<div align="left"><font face="Arial" size="2">Via Roma, 64</font></div>
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<div align="left"><font face="Arial" size="2">"If you think you're
too small to make a change, try sleeping with a mosquito"</font></div>
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<br>
<pre class="moz-signature" cols="72">--
........................................................
--
Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:luca.mollica@ibs.fr">luca.mollica@ibs.fr</a> (<a class="moz-txt-link-abbreviated" href="mailto:lucamollica@gmail.com">lucamollica@gmail.com</a>)
Telephone: +33.438783889
--
Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of cigarettes, it's dark, and we're wearing sunglasses.
Jake: Hit it.
(The Blues Brothers)
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