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Guten Tag, Herr Bert!<span -moz-smiley="s1"><span> :-) </span></span><br>
<br>
Thank you for your help!<br>
But. I've tried to do the EM procedure (first - steep, second - CG), I've
done it repeatedly, but I can't to get the max. force smaller than N.NNNe+03.
I've written the nsteps 10 000, emtol 0.1, emstep 0.01 in the em.mdp. MDRUN
reports:<br>
<br>
Conjugate gradients:<br>
Tolerance = 1.00000e-01<br>
Starting Energy = -1.806502929687500e+04<br>
F-Norm = 2.86931e+03<br>
<br>
Negative w: -6.317044878279e+15<br>
z= -7.175720000000e+07<br>
gpa= 2.911606067096e+07, gpb= 3.938080970864e+08<br>
a= 0.000000000000e+00, b= 4.470657231392e-06<br>
EpotA= -1.817659960938e+04, EpotB= -1.743941601562e+04<br>
Negative number for sqrt encountered (-6317044878278656.000000)<br>
Terminating minimization<br>
<br>
writing lowest energy coordinates.<br>
Maximum force: 6.26841e+03<br>
<br>
Conjugate Gradients did not converge in 10000 steps <br>
{*usually mdrun make here about 30-100 steps*}<br>
Function value at minimum = -1.8177e+04<br>
<br>
After several repeat of the EM the value of max force and E pot stops
to change with the next repeat.<br>
What can you advise in this case? Maybe, the temperature must be decreased?<br>
Or another way: the following advise in Manual is given. To run MD at the
high temperature for a while, and then quench it slowly down to required t.
When do this repeatedly, the global energy minimum <i>may be</i> discovered...<br>
I'll be glad for any advises!<br>
Thank you in advance!<br>
<br>
Oleg.<br>
<br>
Bert de Groot wrote:<br>
<blockquote type="cite" cite="mid:3CA1E580.2248CFE8@gwdg.de">
<pre wrap="">Oleg Katchanov wrote:<br><br></pre>
<blockquote type="cite">
<pre wrap="">I have some problems with a Normal Mode analysis. <br><br><br>editconf -f MOL.gro -o MOL.gro<br>grompp -f em.mdp -c MOL.gro -p MOL.top -o MOL_em.tpr<br>#integrator steep in em.mdp;<br></pre>
</blockquote>
<pre wrap=""><!----><br>it's better to take cg for the later stages of minimization. Remember that<br>for NM, you need to have a fully minimised system (ie a maximal force<br>smaller than approx 0.01), steep is not efficient after the first 100 steps<br>or so. <br><br><br></pre>
<pre wrap=""><br></pre>
</blockquote>
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