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<DIV><FONT size=1></FONT>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 translational and three rotational dimensions of freedom of the
whole system, they should be zero (theoretically) or at least not
much different from zero (e.g: 1e-3 or -1e-3). But in my problem, I
encountered some negative values that are much different from zero, as
I listed before. </DIV>
<DIV> </DIV>
<DIV>And I have used the g_nmtraj_d to generate and visualize the modes
corresponding to those negative eigenvalues, and I found that
those modes were neither translational nor rotational movements
-- they were actually "oscillational movements". It is unreasonable.
So I guess there might be something wrong in my calculation. But, I still can
not figure out what is wrong, even after I discussed with members in my group
this morning.</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>
<DIV><FONT face=Arial size=1></FONT>
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</FONT></DIV>
<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 17:54:51</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">Hi,<BR><BR>But the 6 negative eigenvalues just
corresponds to the 3 translational and 3 rotational<BR>degrees of freedom of the
whole system, or not?<BR>You can check this by looking at the eigenvectors with
g_anaeig.<BR><BR>Berk<BR></DIV><BR><BR>
<BLOCKQUOTE>
<HR id=EC_stopSpelling>
Date: Fri, 25 Apr 2008 13:55:08 +0800<BR>From: silvester.thu@gmail.com<BR>To:
gmx-users@gromacs.org<BR>Subject: [gmx-users] negative eigenvalues occured and
not "nearly zero"<BR><BR>
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<DIV><FONT face=Verdana><FONT size=2>Hello gmx-users:</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2></FONT></FONT> </DIV>
<DIV><FONT face=Verdana><FONT size=2>I'm recently using Normal Mode
Analysis(NMA) of GROMACS package to calculate the foundamental frequency of
graphite systems. But I got some results that are unexplainable, and I can not
continue my work now. </FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2></FONT></FONT> </DIV>
<DIV><FONT face=Verdana size=2>For all the examples below, I use the double
precision GROMACS functions: grompp_d, mdrun_d, and g_nmeig_d. For the EM
part, I used the conjugated-gradients algorism, and for the NMA
part, I used "nm" integrator and included the full precision structure file:
em.trr into the .tpr input file.</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>For the systems that I applied no
restraints, the first six eigenvalues should be zero, or at
least "nearly zero" if we considering the accuracy of numerical
calculating. But the typical first twelve eigenvalues I got have the
values below:</FONT></DIV>
<DIV><FONT face=Verdana size=2>(after EM, the Fmax<5e-4)</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV> 1
-0.37993<BR> 2
-0.335177<BR> 3
-0.206887<BR> 4
-0.111813<BR> 5
-0.0381566<BR> 6
-0.0211911<BR> 7
0.0189381<BR> 8
0.0370517<BR> 9
0.0385126<BR> 10
0.093188<BR> 11
0.132927<BR> 12
0.169143</DIV>
<DIV> </DIV>
<DIV><FONT face=Verdana size=2>the first eigenvalue</FONT> has larger absolute
value than the 7th eigenvalue, which should not happen for an
unrestrained system. WHY the first six eigenvalues are not zero or nearly
zero? I guess there might by something wrong in my input files, but
I can not figure out where it is. By the way, the topology files and
coordinate files are surely correct.</DIV>
<DIV> </DIV>
<DIV>Another problem is:</DIV>
<DIV>For the system that I applied restraints to, which removed the
translation and rotation about the center of mass, the eigenvalues should be
all positive. But I still found that negative values occured. </DIV>
<DIV>
<DIV> 1
-0.135621<BR> 2
-0.0745555<BR> 3
-0.0390086<BR> 4
-0.0108285<BR> 5
0.0101438<BR> 6
0.0553579<BR>
7
0.146471<BR>
8
0.162898<BR>
9 0.344921<BR>
10 0.396553<BR>
11 0.486316<BR>
12 0.544625</DIV></DIV>
<DIV>WHY? </DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>If anyone used the NMA of GROMACS before and
got correct output, it will be very helpful if you can send me your parameters
or input files or give me some advice. If you need any more information,
please e-mail me.</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana><FONT size=2>I really need your help,
thanks.</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2></FONT></FONT> </DIV>
<DIV><FONT face=Verdana><FONT size=2>Yours Sincerely</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2></FONT></FONT> </DIV>
<DIV><FONT face=Verdana><FONT size=2>Yue Shao</FONT></FONT></DIV>
<DIV><FONT face=Verdana></FONT> </DIV>
<DIV><FONT face=Verdana>E-mail: silvester.thu@gmail.com</FONT></DIV>
<DIV><FONT face=Verdana></FONT> </DIV>
<DIV align=left><FONT face=Verdana><FONT size=2>
<HR style="WIDTH: 122px; HEIGHT: 2px" SIZE=2>
</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT color=#c0c0c0><FONT
size=2></FONT></FONT></FONT></DIV>
<DIV>
<DIV><FONT face=Verdana><FONT color=#c0c0c0><FONT size=2>
<DIV><FONT
size=1>___________________________________________________________________________</FONT></DIV>
<DIV><FONT
size=1>___________________________________________________________________________</FONT></DIV>
<DIV><FONT face=Arial size=1></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><STRONG></STRONG></FONT> </DIV></FONT></FONT></FONT></DIV></DIV></BLOCKQUOTE><BR>
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