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On 29/12/2011 8:24 PM, Zahra M wrote:
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<div><span>Sorry ...I forget to announce that my potential
energy is positive, is it logical?<br>
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No.<br>
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<hr size="1"> <b><span style="font-weight:bold;">From:</span></b>
Zahra M <a class="moz-txt-link-rfc2396E" href="mailto:s_zahra_mousavi@yahoo.com"><s_zahra_mousavi@yahoo.com></a><br>
<b><span style="font-weight: bold;">To:</span></b>
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org">"gmx-users@gromacs.org"</a> <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Thursday, December 29, 2011 12:52 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
positive potential energy<br>
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<div>Hi dear all</div>
<div>I'm simulating a system containing CNT, when I
put CNT in a unit cell and want to run energy
minimization in a vacuum, I encounter with such an
error: "The optimal PME mesh load for parallel
simulations is below 0.5 and for highly parallel
simulations between 0.25 and 0.33, for higher
performance, increase the cut-off and the PME grid
spacing", after running grompp. I've tried a lot of
numbers for cut-off radius ,but I didn't get any
result, at last I changed the coulomb type from PME
to Cut-off, and it worked, I want to know if my
results will be reasonable in this case or not, and
how to solve that error.</div>
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<br>
It's not an error, but an advisory about your performance, and
doesn't matter for EM in vacuo which will only run for a few
seconds. Using a plain cut-off is unreasonable by definition, but
doesn't matter for EM in vacuo. Otherwise, you should note that the
suggestion is to "increase the cut-off *and* the PME grid spacing,"
not just one of them.<br>
<br>
Mark<br>
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<div>thank you in advanced</div>
<div>Bests</div>
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<div>-Zahra<br>
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