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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>When you try to minimise, it will typically tell you the worst
offending atoms in your system. Which you can then check visually using VMD
etc and try and work out why it is an issue. Then you can adjust how the
system was set up to fix the issue.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Also, if you just look at the system visually (though can be an
issue with larger systems) if there is something that is really out of place,
it can be easy to spot. Such as two molecules too close, interlocked, or
severely distorted.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Drug Delivery, Disposition and Dynamics</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>
</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@pharm.monash.edu.au<br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Lum Nforbi<br>
<b>Sent:</b> Friday, 20 November 2009 9:19 AM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] How to check for bad contacts<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hello,<br>
<br>
How do you check for bad contacts in a system that cannot be minimized?<br>
<br>
Thanks,<br>
Lum <o:p></o:p></p>
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