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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></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>Yours Sincerely</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>Yue Shao</FONT></DIV>
<DIV> </DIV>
<DIV>E-mail: silvester.thu@gmail.com</DIV>
<DIV> </DIV>
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<DIV><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></DIV></FONT></DIV></FONT></BODY></HTML>