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<DIV><FONT size=1></FONT>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><FONT color=#0000ff size=2></FONT> </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><FONT color=#0000ff size=2><FONT color=#000000
size=3></FONT></FONT> </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><FONT color=#0000ff size=2><FONT color=#000000
size=3></FONT></FONT> </DIV>
<DIV><FONT color=#0000ff size=2><FONT color=#000000 size=3>Thanks a lot for your
attentions!</FONT></DIV>
<DIV><BR></FONT> </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>
<DIV align=left>
<DIV align=left><FONT face=Verdana size=2>
<HR style="WIDTH: 122px; HEIGHT: 2px" SIZE=2>
</FONT></DIV></DIV>
<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>
<DIV><FONT face=Arial size=1></FONT>
<DIV><FONT face=Verdana size=2>
<HR>
</FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发件人：</STRONG> Mark
Abraham</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发送时间：</STRONG>
2008-04-25 19:11:14</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>silvester.thu wrote:</DIV>
<DIV>> Hi Berk, thanks for your reply,
but there are still problems.</DIV>
<DIV>> </DIV>
<DIV>> While the first six eigenvalues
are corresponding to the three </DIV>
<DIV>> translational and three rotational
dimensions of freedom of the whole
</DIV>
<DIV>> system, they should be zero
(theoretically) or at least not </DIV>
<DIV>> much different from zero (e.g:
1e-3 or -1e-3). But in my problem,
I </DIV>
<DIV>> encountered some negative values that
are much different from zero, as I
</DIV>
<DIV>> listed before. </DIV>
<DIV>> </DIV>
<DIV>> And I have used the g_nmtraj_d
to generate and visualize the modes
</DIV>
<DIV>> corresponding to those negative
eigenvalues, and I found that those
</DIV>
<DIV>> modes were neither translational nor
rotational movements -- they were </DIV>
<DIV>> actually "oscillational movements". It
is unreasonable. So I guess there
</DIV>
<DIV>> might be something wrong in my
calculation. But, I still can not
figure </DIV>
<DIV>> out what is wrong, even after
I discussed with members in my group
this </DIV>
<DIV>> morning.</DIV>
<DIV> </DIV>
<DIV>I don't have much experience in such
a calculation with an MM force</DIV>
<DIV>field, but such Hessian eigenvalues in
quantum chemistry indicate that</DIV>
<DIV>you are at some non-minimum stationary
point. That seems unlikely for an</DIV>
<DIV>MM EM calculation, unless the PES is
very flat. I can't guess what</DIV>
<DIV>"oscillational movements" are, but if you
perturb the system in the</DIV>
<DIV>direction of that eigenvector (easy if
it's mostly on a few atoms,</DIV>
<DIV>otherwise just add a suitable multiple
of the eigenvector to the atom</DIV>
<DIV>coordinate vector) you can see if you
get into the range of a suitable</DIV>
<DIV>local minimum, or return to your
existing stationary point.</DIV>
<DIV> </DIV>
<DIV>Mark</DIV>
<DIV>_______________________________________________</DIV>
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