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<p style="margin-bottom: 0in;"> Dear All, </p>
<p style="margin-bottom: 0in;"> I am trying to do a
normal modes analysis using GROMACS. The system I look at is a
tetra-peptide embedded in a DMPC membrane, solvated in water. After a
MD I took the last conformation (of the all system) and minimize it.
First using steepest descent, them moving to conjugate gradient,
finishing with l-bfgs (emtol = 0.0001 and emstep = 0.01). The system
did not converged to the emtol but to machine precision, and I got
the usual message:</p>
<p style="margin-bottom: 0in;"><i>Stepsize too small, or no change in
energy.</i></p>
<p style="margin-bottom: 0in;"><i>Converged to machine precision,</i></p>
<p style="margin-bottom: 0in;"><i>but not to the requested precision
Fmax < 0.0001</i></p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;"><i>writing lowest energy coordinates.</i></p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;"><i>Low-Memory BFGS Minimizer converged
to machine precision in 1103 steps,</i></p>
<p style="margin-bottom: 0in;"><i>but did not reach the requested Fmax
< 0.0001.</i></p>
<p style="margin-bottom: 0in;"><i>Potential Energy =
-3.34893104062525e+05</i></p>
<p style="margin-bottom: 0in;"><i>Maximum force = 5.53432484050007e+01
on atom 9679</i></p>
<p style="margin-bottom: 0in;"><i>Norm of force = 1.87035735871414e+00</i></p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;">As all can imagine, trying to calculate
the normal modes I got:</p>
<p style="margin-bottom: 0in;"><i>Maximum force:
8.61232e+02</i></p>
<p style="margin-bottom: 0in;"><i>Maximum force
probably not small enough to ensure that you are in a </i>
</p>
<p style="margin-bottom: 0in;"><i>energy well. Be
aware that negative eigenvalues may occur when the</i></p>
<p style="margin-bottom: 0in;"><i>resulting
matrix is diagonalized.</i></p>
<p style="margin-bottom: 0in;"><br>
Result from this is the obvious
question should I pay attention to it, and if yes how can I over come
it?</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;">Second question, which might look
stupid to you, is how to read the results from g_nmeig_double. I
though the results will be the wavenumber or vibration frequencies,
how do I see the results in such a way.</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;"> Thanks all.</p>
<p style="margin-bottom: 0in;"><br>
</p>
<p style="margin-bottom: 0in;">BTW I used both DFLEX_SPC and DFLEXIBL,
the results are the same. I know that this is because I use the
Gromacs Forcefield, but I guess some might offer it as a solution.</p>
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