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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I have been able to obtain a radial
distribution function using “g_rdf -f traj.xtc -n index.ndx -o -com -xy
-b 100” and I have been working with trjorder to get the 3 of water
molecules with in the tube, the best results so far have been with looking at
the center of mass of the CNT, although I can not expand the radius enough to
get the whole inside of the tube with out including water outside the tube. Is
there a way to get this to work as a cylinder instead of a sphere? Or many put
some other reference group in that will have no effect on the simulation and
have a fixed position (i.e. along the center of the cylinder)?<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'>Thank you for help,<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'>~Christopher Stiles<o:p></o:p></span></font></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceType w:st="on"><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>College</span></font></st1:PlaceType><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'> of <st1:PlaceName
w:st="on">Nanoscale</st1:PlaceName></span></font></st1:place><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> Science and Engineering (CNSE)<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'>State <st1:PlaceType w:st="on">University</st1:PlaceType>
of <st1:PlaceName w:st="on">New York</st1:PlaceName>, <st1:place w:st="on"><st1:City
w:st="on">Albany</st1:City>, <st1:State w:st="on">New York</st1:State> <st1:PostalCode
w:st="on">12203</st1:PostalCode>, <st1:country-region w:st="on">USA</st1:country-region></st1:place><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 class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Christopher Stiles<br>
<b><span style='font-weight:bold'>Sent:</span></b> Sunday, August 05, 2007
11:57 PM<br>
<b><span style='font-weight:bold'>To:</span></b> '<st1:PersonName w:st="on">Discussion
list for GROMACS users</st1:PersonName>'<br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] Analysis of
CNT in water solution</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I am trying to look at the # of water molecules within the
CNT as a function of time and I was wondering if there was another app like
Trjorder that maybe instead of using a group of molecules as the reference you
could use coordinates i.e. the axis of the CNT, or if there is a better way to
go about this?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Information on the setup; it is a 2.81700
2.81700 3.35410 box with a ( 6 , 6 ) CNT (centered in the box) and
811 spc216 molecules and it is at 300k and run for 200ps.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thank you for help,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>~Christopher Stiles<o:p></o:p></span></font></p>
<p class=MsoNormal><st1:place w:st="on"><st1:PlaceType w:st="on"><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>College</span></font></st1:PlaceType><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> of <st1:PlaceName
w:st="on">Nanoscale</st1:PlaceName></span></font></st1:place><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'> Science and
Engineering (CNSE)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>State <st1:PlaceType w:st="on">University</st1:PlaceType> of
<st1:PlaceName w:st="on">New York</st1:PlaceName>, <st1:place w:st="on"><st1:City
w:st="on">Albany</st1:City>, <st1:State w:st="on">New York</st1:State> <st1:PostalCode
w:st="on">12203</st1:PostalCode>, <st1:country-region w:st="on">USA</st1:country-region></st1:place><o:p></o:p></span></font></p>
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