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<DIV>Thanks David!</DIV>
<DIV> </DIV>
<DIV>I have set constraints=none in .mdp file, and include the .trr
file with -t option </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> David van der
Spoel</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发送时间：</STRONG>
2008-04-25 19:44:01</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>> </DIV>
<DIV>> Thanks Mark.</DIV>
<DIV>> I also have doubted that the
system was not at the minium
stationary </DIV>
<DIV>> point before, because I searched
the mailing-list archive and found the
</DIV>
<DIV>> description below:</DIV>
<DIV>> </DIV>
<DIV>> I have checked the first
eigenvalues in .xvg files, some of
them really </DIV>
<DIV>> large.</DIV>
<DIV>> For example, a 88 amino acid
protein (PDB ID=1krn), there are 79
amino</DIV>
<DIV>> acid coordinates in the PDB file.
After EM, the Max force < 1e-9,
while the</DIV>
<DIV>> first 12 eigenvalues g_nmeig_d worked
out are:</DIV>
<DIV>> 1
0.000438558</DIV>
<DIV>> 2
-0.000683771</DIV>
<DIV>> 3
-0.00292664</DIV>
<DIV>> 4
0.00597364</DIV>
<DIV>> 5
0.00817211</DIV>
<DIV>> 6
-0.0114438</DIV>
<DIV>> 7
1.58334</DIV>
<DIV>> 8
1.80916</DIV>
<DIV>> 9
2.04356</DIV>
<DIV>> 10
2.6188</DIV>
<DIV>> 11
2.87512</DIV>
<DIV>> 12
3.44095</DIV>
<DIV>> </DIV>
<DIV>> The author of this description was
describing another problem which was </DIV>
<DIV>> different from my question. But
this descripment is helpful for me. In
</DIV>
<DIV>> this description, the author minimized
the energy of the system to reach
</DIV>
<DIV>> the level -- Fmax <1e-9 --
which I do not know how to get
to. I have </DIV>
<DIV>> tried my best to EM, but I
only got Fmax <3e-4. In the mdrun_d
step, </DIV>
<DIV>> there is no warning, while in
the g_nmeig_d step, there is a warning
that</DIV>
<DIV>> </DIV>
<DIV>> /One of the lowest 6 eigenvalues
has a non-zero value.</DIV>
<DIV>> This could mean that the reference
structure was not</DIV>
<DIV>> properly energy minimized./</DIV>
<DIV>> </DIV>
<DIV>> So the system may be not at
the minimum stationary point. How can
I make </DIV>
<DIV>> the system to reach this
point?</DIV>
<DIV> </DIV>
<DIV>Could it be that you used the
coordinates from the .gro file for the
nm</DIV>
<DIV>calculations?</DIV>
<DIV>Since these are rounded they may not
correspond to the energy minimum.</DIV>
<DIV>You can use the grompp -t option
to get binary coordinates.</DIV>
<DIV> </DIV>
<DIV>Also, have you turned off constraints?</DIV>
<DIV> </DIV>
<DIV>> </DIV>
<DIV>> What's more, in the description
above, the first six eigenvalues are
</DIV>
<DIV>> very near to zero, and that
is what I want now, because as I
said </DIV>
<DIV>> before, I can not get such
"nearly zero" eigenvalues.</DIV>
<DIV>> </DIV>
<DIV>> So, if you know how to do
the EM to such a low energy
level, or how to </DIV>
<DIV>> get those "nearly zero" eigenvalues,
please give me some advice or some
</DIV>
<DIV>> examples.</DIV>
<DIV>> </DIV>
<DIV>> Thanks a lot for your
attentions!</DIV>
<DIV>> </DIV>
<DIV>> </DIV>
<DIV>> </DIV>
<DIV>> </DIV>
<DIV>> With my best regards.</DIV>
<DIV>> </DIV>
<DIV>> Yue Shao</DIV>
<DIV>> </DIV>
<DIV>>
2008-04-25</DIV>
<DIV>> </DIV>
<DIV>>
___________________________________________________________________________</DIV>
<DIV>>
___________________________________________________________________________</DIV>
<DIV>> ** </DIV>
<DIV>> *Shao Yue*</DIV>
<DIV>> Institue of Biomechanics and Biomedical
Engineering</DIV>
<DIV>> Department of Engineering Mechanics</DIV>
<DIV>> Tsinghua University</DIV>
<DIV>> P.R. China</DIV>
<DIV>>
____________________________________________________________________________
</DIV>
<DIV>> </DIV>
<DIV>>
____________________________________________________________________________
</DIV>
<DIV>> </DIV>
<DIV>> </DIV>
<DIV>> *发件人：* Mark Abraham</DIV>
<DIV>> *发送时间：* 2008-04-25 19:11:14</DIV>
<DIV>> *收件人：* Discussion list for GROMACS
users</DIV>
<DIV>> *抄送：*</DIV>
<DIV>> *主题：* Re: [gmx-users] negative
eigenvalues occured and not "nearly
zero"</DIV>
<DIV>> </DIV>
<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 </DIV>
<DIV>> three </DIV>
<DIV>> > translational and
three rotational dimensions of
freedom of </DIV>
<DIV>> 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
</DIV>
<DIV>> problem, I </DIV>
<DIV>> > encountered some
negative values that are
much different </DIV>
<DIV>> from zero, as I
</DIV>
<DIV>> > listed before.
</DIV>
<DIV>> > </DIV>
<DIV>> > And I have
used the g_nmtraj_d to
generate and visualize </DIV>
<DIV>> the modes </DIV>
<DIV>> > corresponding to
those negative eigenvalues, and
I found </DIV>
<DIV>> that those </DIV>
<DIV>> > modes were
neither translational nor
rotational movements -- </DIV>
<DIV>> they were </DIV>
<DIV>> > actually "oscillational
movements". It is
unreasonable. So I </DIV>
<DIV>> guess there </DIV>
<DIV>> > might be
something wrong in my
calculation. But, I still
</DIV>
<DIV>> can not figure
</DIV>
<DIV>> > out what is
wrong, even after I
discussed with members in
</DIV>
<DIV>> my group this
</DIV>
<DIV>> > morning.</DIV>
<DIV>> </DIV>
<DIV>> I don't have much
experience in such a
calculation with an MM </DIV>
<DIV>> force</DIV>
<DIV>> field, but such Hessian
eigenvalues in quantum
chemistry </DIV>
<DIV>> indicate that</DIV>
<DIV>> you are at some
non-minimum stationary point. That
seems </DIV>
<DIV>> unlikely for an</DIV>
<DIV>> MM EM calculation, unless
the PES is very
flat. I can't guess </DIV>
<DIV>> what</DIV>
<DIV>> "oscillational movements" are,
but if you perturb the
system in </DIV>
<DIV>> the</DIV>
<DIV>> direction of that
eigenvector (easy if it's
mostly on a few </DIV>
<DIV>> atoms,</DIV>
<DIV>> otherwise just add a
suitable multiple of the
eigenvector to </DIV>
<DIV>> the atom</DIV>
<DIV>> coordinate vector) you
can see if you get
into the range of
</DIV>
<DIV>> a suitable</DIV>
<DIV>> local minimum, or return
to your existing stationary
point.</DIV>
<DIV>> </DIV>
<DIV>> Mark</DIV>
<DIV>> _______________________________________________</DIV>
<DIV>> gmx-users mailing list
gmx-users@gromacs.org</DIV>
<DIV>> <A
href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV>
<DIV>> Please search the archive
at <A
href="http://www.gromacs.org/search">http://www.gromacs.org/search</A>
before </DIV>
<DIV>> posting!</DIV>
<DIV>> Please don't post
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list. Use the </DIV>
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<DIV>> </DIV>
<DIV>> </DIV>
<DIV>>
------------------------------------------------------------------------</DIV>
<DIV>> </DIV>
<DIV>> _______________________________________________</DIV>
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<DIV> </DIV>
<DIV> </DIV>
<DIV>-- </DIV>
<DIV>David van der Spoel, Ph.D.</DIV>
<DIV>Molec. Biophys. group, Dept. of Cell
& Molec. Biol., Uppsala University.</DIV>
<DIV>Box 596, 75124 Uppsala, Sweden. Phone:
+46184714205. Fax: +4618511755.</DIV>
<DIV>spoel@xray.bmc.uu.se spoel@gromacs.org <A
href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A></DIV>
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