Payman,<br><br>Such little charge cannot produce large energies, so it seems you should run EM first and everything will be OK with your simulation.<br><br>As far as understand non-zero charge is a resuts of averaging errors (during grompp!), you cannot remove this warning.<br>
<br>~ Vitaly<br><br><div class="gmail_quote">On Wed, Jul 22, 2009 at 3:04 AM, Payman Pirzadeh <span dir="ltr"><<a href="mailto:ppirzade@ucalgary.ca">ppirzade@ucalgary.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">OK! Thanks for the tips on thermostat.</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">I multiplied my .gro file by using the command “genconf”. My
original box has non-zero charge, but the generated bigger box has some
charges:</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">NOTE 2 [file sixsitemodel.top, line 8]:</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> System has non-zero total charge: -1.220703e-04</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Then, during minimization, the system experiences a large
positive potential and infinite force. Is there a technicality in using “genconf”
that I am missing? Doesn’t it read the dimensions of the box from .gro file to
make sure no particles are overlapping with the original box? Or no particle is
coming from the new one in the old one?</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Payman</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
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<p><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;">
<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] <b>On
Behalf Of </b>Vitaly V. Chaban<br>
<b>Sent:</b> July 21, 2009 4:53 PM<br>
<b>To:</b> <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<b>Subject:</b> [gmx-users] Re: reliability of NOTES</span></p>
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<p> </p>
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<p><br>
Hello,<br>
I am trying to prepare the input files for an MD run. After running grompp,<br>
I received the following note:<br>
<br>
NOTE 1 [file npt.mdp, line unknown]:<br>
The Berendsen thermostat does not generate the correct kinetic energy<br>
distribution. You might want to consider using the V-rescale thermostat.<br>
<br>
How reliable this note is? </p>
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<p><br>
It's true.<br>
</p>
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<p>And how can I implement V-rescale thermostat in y<br>
input file (I found nothing in the manual).</p>
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<p><br>
Substitute "berendsen" with "V-rescale" in the mdp file. </p>
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<p style="margin-bottom: 12pt;"><br>
Also, when I changed the thermostat to nose-hoover, it said that it can not<br>
be used with Berendsen barostat. Why?</p>
</blockquote>
</div>
<p>C'est la vie...<br>
<br clear="all">
<br>
-- <br>
Vitaly V. Chaban, Ph.D. (ABD)<br>
School of Chemistry<br>
V.N. Karazin Kharkiv National University<br>
Svoboda sq.,4, Kharkiv 61077, Ukraine<br>
email: <a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a>,<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a><br>
skype: vvchaban, mob.: +38-097-8259698 <br>
<a href="http://www-rmn.univer.kharkov.ua/chaban.html" target="_blank">http://www-rmn.univer.kharkov.ua/chaban.html</a><br>
===================================<br>
!!! Looking for a postdoctoral position !!!<br>
===================================</p>
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