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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="mso-ansi-language: EN-US"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">Dear users,<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p><FONT color=#000000> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>I would like to calculate the mean square displacement.<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>Using the <o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p><FONT color=#000000> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>g_msd -f traj.xtc -s input.tpr <SPAN style="mso-spacerun: yes"> </SPAN>-n index.ndx -o msd.xvg<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p><FONT color=#000000> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>I get </FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p><FONT color=#000000> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT color=#000000><?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:place w:st="on"><st1:City w:st="on"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US">Reading</SPAN></st1:City></st1:place><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"> file input.tpr, VERSION 3.3.2(single precision)<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT color=#000000><st1:place w:st="on"><st1:City w:st="on"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US">Reading</SPAN></st1:City></st1:place><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"> file input.tpr, VERSION 3.3.2(single precision)<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>Group <SPAN style="mso-tab-count: 1"> </SPAN>0(<SPAN style="mso-tab-count: 1"> </SPAN>C) has <SPAN style="mso-tab-count: 1"></SPAN><SPAN style="mso-tab-count: 1"> </SPAN>1 elements<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>There is one group in the index<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT color=#000000><st1:place w:st="on"><st1:City w:st="on"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US">Reading</SPAN></st1:City></st1:place><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"> frame 0 time 0.000<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p><FONT color=#000000> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>The system always freezes here without any warning or error. I have checked my<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>Input files both visually and using gmxcheck, can not find any problem.<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p><FONT color=#000000> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>Thank you very much for your help. I have tried to find the solution in both manuals <o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>and archives (thank you very much for them), you are my last resort.<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p><FONT color=#000000> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>Thank you in advance,<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><o:p><FONT color=#000000> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: EN-US"><FONT color=#000000>Katka Hynstova<o:p></o:p></FONT></SPAN></P><br /><hr />Explore the seven wonders of the world <a href='http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE' target='_new'>Learn more!</a></body>
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