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<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>Dear all,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>I was wondering if someone
could offer some advice?<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>I would like to run an
atomistic langevin dynamics simulation (as I don't want to include water
explicitly). If I add the appropriate langevin dynamics options in the mdp
file, then is there any reason why I shouldn't use explicit counter ions
(unfortunately my protein has an overall charge)?<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>Obviously I would use
periodic boundary conditions so the ions don't wander off.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>Many thanks in advance for
your suggestions/comments,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>-Syma<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p><font size=2 color=navy face="Times New Roman"><span style='font-size:10.0pt;
color:navy'>***********************************************************************<br>
Dr Syma Khalid<br>
RCUK Fellow (Chemical
Biology) <br>
<st1:place w:st="on"><st1:PlaceType w:st="on">School</st1:PlaceType> of <st1:PlaceName
w:st="on">Chemistry</st1:PlaceName></st1:place><br>
<st1:place w:st="on"><st1:PlaceType w:st="on">University</st1:PlaceType> of <st1:PlaceName
w:st="on">Southampton <br>
Highfield
<br>
Southampton</st1:PlaceName></st1:place> phone:
(0)2380-594176<br>
SO17 1BJ email:
S.Khalid@soton.ac.uk
<br>
<st1:country-region w:st="on"><st1:place w:st="on">U.K.</st1:place></st1:country-region><br>
***********************************************************************<br>
</span></font><font color=navy><span style='color:navy'> </span></font><o:p></o:p></p>
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