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<p class=MsoNormal><font size=2 color=navy face="Comic Sans MS"><span
style='font-size:10.0pt;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
color:navy'>Hi,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face="Comic Sans MS"><span
style='font-size:10.0pt;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
color:navy'>I have a MD simulation run of 600ps. To analyze the result, I ran
the <span class=SpellE>g_rms</span> command.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face="Comic Sans MS"><span
style='font-size:10.0pt;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
color:navy'>What has happened though is that the structure has not changed
much, but has translated along the Z axis after around 300ps. Due to this the <span
class=SpellE>g_rms</span> output does not reflect the correct picture of the
structure remaining unchanged after the dynamics run.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face="Comic Sans MS"><span
style='font-size:10.0pt;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face="Comic Sans MS"><span
style='font-size:10.0pt;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
color:navy'>Is there an option (or another command) so that the translation can
be ignored and just the structural changes reflected in the RMS output?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face="Comic Sans MS"><span
style='font-size:10.0pt;font-family:"Comic Sans MS";mso-bidi-font-family:Arial;
color:navy'><o:p> </o:p></span></font></p>
<p class=MsoAutoSig><font size=5 color=navy face="Monotype Corsiva"><span
style='font-size:16.0pt;font-family:"Monotype Corsiva";color:navy;mso-no-proof:
yes'>Madhuri Agashe<o:p></o:p></span></font></p>
<p class=MsoAutoSig><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy;mso-no-proof:yes'>Graduate Research
Assistant,<o:p></o:p></span></font></p>
<p class=MsoAutoSig><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy;mso-no-proof:yes'>Dept. of Bioengineering,<o:p></o:p></span></font></p>
<p class=MsoAutoSig><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy;mso-no-proof:yes'>Clemson University,<br>
Clemson, SC 29631<o:p></o:p></span></font></p>
<p class=MsoAutoSig><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy;mso-no-proof:yes'>Phone: 864-653-4230 (resi)<o:p></o:p></span></font></p>
<p class=MsoAutoSig><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy;mso-no-proof:yes'><span
style='mso-spacerun:yes'>
</span>864-656-1352 (off.)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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