Payman, <br><br>What system fo you try to simulate? How was the initial configuration generated? Did you do EM of the small box before using genconf?<br><br>Anyway, try to decrease the time step (several orders) and start a small (~1000 steps) MD run. If you experience the overlaps of the particles it should help to get a better configuration. - This is to be fast.<br>
<br>Vitaly<br><br><div class="gmail_quote">On Wed, Jul 22, 2009 at 5:18 PM, 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;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Hi Vitaly,</span></p>
<p><span style="font-size: 11pt; color: rgb(31, 73, 125);">Problem is when I minimized the system, the potential energy
will become sth positive of the order of 10^21 and the force experienced by an
atom becomes infinity. This will cause the simulation to crash!</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>
<div style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;"> Vitaly V. Chaban
[mailto:<a href="mailto:vvchaban@gmail.com" target="_blank">vvchaban@gmail.com</a>] <br>
<b>Sent:</b> July 22, 2009 2:20 AM<br>
<b>To:</b> Payman Pirzadeh; <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<b>Subject:</b> Re: genconf</span></p>
</div><div><div></div><div class="h5">
<p> </p>
<p style="margin-bottom: 12pt;">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</p>
<div>
<p>On Wed, Jul 22, 2009 at 3:04 AM, Payman Pirzadeh <<a href="mailto:ppirzade@ucalgary.ca" target="_blank">ppirzade@ucalgary.ca</a>> wrote:</p>
<div>
<div>
<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>
<div style="border-style: solid none none; border-color: -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<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>
</div>
<p> </p>
<div>
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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>
</blockquote>
<div>
<p><br>
It's true.<br>
</p>
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<blockquote style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color rgb(204, 204, 204); border-width: medium medium medium 1pt; margin: 5pt 0cm 5pt 4.8pt; padding: 0cm 0cm 0cm 6pt;">
<p>And how can I implement V-rescale thermostat in y<br>
input file (I found nothing in the manual).</p>
</blockquote>
<div>
<p><br>
Substitute "berendsen" with "V-rescale" in the mdp file. </p>
</div>
<blockquote style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color rgb(204, 204, 204); border-width: medium medium medium 1pt; margin: 5pt 0cm 5pt 4.8pt; padding: 0cm 0cm 0cm 6pt;">
<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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