<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceType"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceName"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PersonName"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
        {font-family:David;
        panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
        {margin:0cm;
        margin-bottom:.0001pt;
        font-size:12.0pt;
        font-family:"Times New Roman";}
a:link, span.MsoHyperlink
        {color:blue;
        text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
        {color:purple;
        text-decoration:underline;}
p.MsoAutoSig, li.MsoAutoSig, div.MsoAutoSig
        {margin:0cm;
        margin-bottom:.0001pt;
        text-align:right;
        direction:rtl;
        unicode-bidi:embed;
        font-size:12.0pt;
        font-family:"Times New Roman";}
span.EmailStyle17
        {mso-style-type:personal-compose;
        font-family:Arial;
        color:windowtext;}
@page Section1
        {size:595.3pt 841.9pt;
        margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.Section1
        {page:Section1;}
/* List Definitions */
@list l0
        {mso-list-id:1550998810;
        mso-list-type:hybrid;
        mso-list-template-ids:-249260230 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l0:level1
        {mso-level-tab-stop:36.0pt;
        mso-level-number-position:left;
        text-indent:-18.0pt;}
@list l0:level2
        {mso-level-tab-stop:72.0pt;
        mso-level-number-position:left;
        text-indent:-18.0pt;}
@list l0:level3
        {mso-level-tab-stop:108.0pt;
        mso-level-number-position:left;
        text-indent:-18.0pt;}
@list l0:level4
        {mso-level-tab-stop:144.0pt;
        mso-level-number-position:left;
        text-indent:-18.0pt;}
@list l0:level5
        {mso-level-tab-stop:180.0pt;
        mso-level-number-position:left;
        text-indent:-18.0pt;}
@list l0:level6
        {mso-level-tab-stop:216.0pt;
        mso-level-number-position:left;
        text-indent:-18.0pt;}
@list l0:level7
        {mso-level-tab-stop:252.0pt;
        mso-level-number-position:left;
        text-indent:-18.0pt;}
@list l0:level8
        {mso-level-tab-stop:288.0pt;
        mso-level-number-position:left;
        text-indent:-18.0pt;}
@list l0:level9
        {mso-level-tab-stop:324.0pt;
        mso-level-number-position:left;
        text-indent:-18.0pt;}
ol
        {margin-bottom:0cm;}
ul
        {margin-bottom:0cm;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=EN-US link=blue vlink=purple>
<div class=Section1 dir=RTL>
<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> </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 on gromacs 3.2.1, I get different charts (msd vs. t) and
different values for the diffusion coefficient. What do you
recommend to "trust", 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 –mol I get
different values for D and again different charts of msd vs. time.
Can you clarify more about the option –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> </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> </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> </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> </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:
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:
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:
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> </o:p></span></font></p>
</div>
</body>
</html>