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<DIV><FONT size=1></FONT>Hi Berk,</DIV>
<DIV> </DIV>
<DIV>I am working on a system of graphenes. As the topology of graphite is
known and simple, I assume that the system can reach a very low energy
level. However, I still not know how to minimize the energy of such a system
containing protein to Fmax<1e-9, as the description I quoted
before. Or did I misunderstand the description of that author I
mentioned before?</DIV>
<DIV>So, could the graphene system I am working on reach such a low energy level
like 1e-9? I have tried every way I can figure out, but they did not work.</DIV>
<DIV>By the way, I used CG integerator.</DIV>
<DIV> </DIV>
<DIV>Thanks for your attention!</DIV>
<DIV><FONT face=Verdana color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Verdana color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Verdana color=#000000 size=2>With my best regards.</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT><FONT color=#000000></FONT> </DIV>
<DIV><FONT face=Verdana color=#000000 size=2>Yue Shao</FONT></DIV>
<DIV><FONT face=Verdana color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Verdana color=#0000ff
size=2>
2008-04-25</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
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<DIV><FONT
size=1>___________________________________________________________________________</FONT></DIV>
<DIV><FONT
size=1>___________________________________________________________________________</FONT></DIV>
<DIV><FONT face=Arial size=1><STRONG></STRONG></FONT> </DIV>
<DIV><FONT face=Arial size=2><STRONG>Shao Yue</STRONG></FONT></DIV>
<DIV><FONT face=Arial size=2>Institue of Biomechanics and Biomedical
Engineering</FONT></DIV>
<DIV><FONT face=Arial size=2>Department of Engineering Mechanics</FONT></DIV>
<DIV><FONT face=Arial size=2>Tsinghua University</FONT></DIV>
<DIV><FONT face=Arial size=2>P.R. China</FONT></DIV>
<DIV>
<DIV><FONT
size=1>____________________________________________________________________________</FONT></DIV>
<DIV><FONT
size=1>____________________________________________________________________________</FONT></DIV></DIV>
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<DIV><FONT face=Verdana><FONT size=2><STRONG>发件人：</STRONG> Berk
Hess</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发送时间：</STRONG>
2008-04-25 20:38:25</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>收件人：</STRONG> Discussion list for
GROMACS users</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>抄送：</STRONG> </FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>主题：</STRONG> RE: [gmx-users]
negative eigenvalues occured and not "nearly zero"</FONT></FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>
<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>
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