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<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear all,<o:p></o:p></span></font></p>

<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<ol style='margin-top:0cm' start=1 type=1>
 <li class=MsoNormal dir=LTR style='mso-list:l0 level1 lfo1'><font size=2
     face=Arial><span style='font-size:10.0pt;font-family:Arial'>I have an .xtc
     and .tpr files of a simulation (protein, ligand, ions and spc216 water)
     which were performed on gromacs 3.2.1 two years ago. When I run g_msd
     based on these files on a specific water molecule in gromacs 3.3.1
     and&nbsp; on gromacs 3.2.1, I get different charts (msd vs. t) and
     different values for the diffusion coefficient.&nbsp; What do you
     recommend to &quot;trust&quot;, the new version results or should I
     perform all analysis procedure on these files on gromacs 3.2.1?</span></font>
     <font size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></li>
 <li class=MsoNormal dir=LTR style='mso-list:l0 level1 lfo1'><font size=2
     face=Arial><span style='font-size:10.0pt;font-family:Arial'>When I run
     g_msd on a specific water residue with and without the option &#8211;mol I get
     different values for D and again different charts of msd vs. time.&nbsp;
     Can you clarify more about the option &#8211;mol? <o:p></o:p></span></font></li>
</ol>

<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal dir=LTR style='margin-left:36.0pt'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Thank you all,<o:p></o:p></span></font></p>

<p class=MsoNormal dir=LTR style='margin-left:36.0pt'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal dir=LTR style='margin-left:36.0pt'><st1:PersonName w:st="on"><font
 size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>Yossi
 Tsfadia </span></font></st1:PersonName><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>

<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoAutoSig dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Dr.
Yossi Tsfadia<o:p></o:p></span></font></p>

<p class=MsoAutoSig dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><st1:place w:st="on"><st1:PlaceName w:st="on"><font size=3
  face="Times New Roman"><span style='font-size:12.0pt'>Tel</span></font></st1:PlaceName>
 <st1:PlaceName w:st="on">Aviv</st1:PlaceName> <st1:PlaceType w:st="on">University</st1:PlaceType></st1:place><o:p></o:p></p>

<p class=MsoAutoSig dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Faculty
of Life Sciences<o:p></o:p></span></font></p>

<p class=MsoAutoSig dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Tel:&nbsp;&nbsp;&nbsp;
3-972-6405766<o:p></o:p></span></font></p>

<p class=MsoAutoSig dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Fax:&nbsp;&nbsp;
3-972-6405146<o:p></o:p></span></font></p>

<p class=MsoAutoSig dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>E-mail:&nbsp;
yossit@tauex.tau.ac.il<o:p></o:p></span></font></p>

<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>

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