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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><blockquote><hr id="EC_stopSpelling">Date: Fri, 25 Apr 2008 19:31:15 +0800<br>From: silvester.thu@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: Re: Re: [gmx-users] negative eigenvalues occured and not "nearly zero"<br><br>
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<div>Thanks Mark. </div>
<div>I also have doubted that the system was not at the minium stationary
point before, because I searched the mailing-list archive and
found the description below:</div>
<div> </div>
<div><font color="#0000ff" size="2">I have checked the first eigenvalues in .xvg
files, some of them really large.<br>For example, a 88 amino acid protein (PDB
ID=1krn), there are 79 amino <br>acid coordinates in the PDB file. After EM, the
Max force< 1e-9, while the<br>first 12 eigenvalues g_nmeig_d worked out
are:<br> 1
0.000438558<br> 2
-0.000683771<br> 3
-0.00292664<br> 4
0.00597364<br> 5
0.00817211<br> 6
-0.0114438 <br>
7
1.58334<br>
8
1.80916<br>
9 2.04356<br>
10
2.6188<br> 11
2.87512<br> 12
3.44095</font></div>
<div> </div>
<div><font color="#0000ff" size="2"><font color="#000000" size="3">The author of this
description was describing another problem which was different from my question.
But this descripment is helpful for me. In this description, the author
minimized the energy of the system to reach the level -- Fmax<1e-9 -- which I
do not know how to get to. I have tried my best to EM, but I only got
Fmax<3e-4. In the mdrun_d step, there is no warning, while in the g_nmeig_d
step, there is a warning that </font></font></div>
<div> </div>
<div><font color="#0000ff" size="2"><font color="#000000" size="3"><em>One of the lowest
6 eigenvalues has a non-zero value.<br>This could mean that the reference
structure was not<br>properly energy minimized.</em></font></font></div>
<div> </div>
<div>So the system may be not at the minimum stationary point. How can I make
the system to reach this point?</div>
<div> </div>
<div><font color="#0000ff" size="2"><font color="#000000" size="3">What's more, in the
description above, the first six eigenvalues are very near to zero, and that is
what I want now, because as I said before, I can not get such "nearly zero"
eigenvalues.</font></font></div>
<div> </div>
<div><font color="#0000ff" size="2"><font color="#000000" size="3">So, if you know how
to do the EM to such a low energy level, or how to get those "nearly zero"
eigenvalues, please give me some advice or some examples.</font></font></div>
<div> </div>
<div><font color="#0000ff" size="2"><font color="#000000" size="3">Thanks a lot for your
attentions!</font></font><br><br></div></blockquote>I assume you are already using CG or LBFGS.<br><br>You did not describe your system, but if you for instance have water molecules around<br>a protein, it becomes very difficult to minimize to low forces.<br><br>Berk.<br><br><div><br></div><blockquote>
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