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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi,<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'>I am running AFM pulling simulations on an integrin-RGD
system. I have tried running the exact same simulation in version 3.3.1 and
version 3.3.2, and I am getting a large VCM message in 3.3.2, but not 3.3.1. Here
are the cases that I have tried:<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 style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>Version
3.2.1: The integrin receptor has two subunits, alpha and beta. If I do com
motion removal on these two separately (i.e. comm._grps = alpha beta), with tc_grps
= Protein Other, the simulation finishes normally.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>Version:3.2.2:
Same conditions as above, but I get the following message in the log file. This
happens even if I use the exact same input files as with version 3.2.1. It
starts at the beginning of the simulation and continues to print this message
at every output timestep.<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'>Large VCM(group rest): 0.00001, -0.00002,
-0.00000, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): 0.00001, -0.00003,
-0.00000, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): -0.00000, -0.00003, -0.00000,
T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): -0.00000, -0.00003,
0.00000, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): -0.00001, -0.00004,
0.00000, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): -0.00001, -0.00004, 0.00001,
T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): -0.00001, -0.00004,
0.00001, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): -0.00001, -0.00004,
0.00001, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): -0.00001, -0.00003,
0.00002, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): -0.00001, -0.00003,
0.00002, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): -0.00001, -0.00003,
0.00002, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): 0.00000, -0.00003,
0.00002, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): 0.00001, -0.00003,
0.00002, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): 0.00002, -0.00003,
0.00002, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): 0.00002, -0.00002,
0.00002, T-cm: inf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Large VCM(group rest): 0.00003, -0.00002,
0.00002, T-cm: inf<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 style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>3)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>Version
3.2.2: If I try comm._grps = alpha beta and tc_grps = alpha beta Other, this message
does not appear.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.25in'><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'>Question 1: What has changed between version 3.2.1 and 3.2.2
that is causing this message to appear? I can’t find information about
this on the website.<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'>Question 2: Is it an adequate solution to make comm._grps
the same as tc-grps? Can somebody explain why I no longer have the VCM problem
in this case?<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 very much,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Ranjani<o:p></o:p></span></font></p>
<div style='mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.5pt;
padding:0in 0in 1.0pt 0in'>
<p class=MsoNormal style='border:none;padding:0in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
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<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'>Ranjani Krishnan<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Graduate student, Department of Biological Engineering<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Massachusetts Institute of Technology<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>ranjanik@mit.edu<o:p></o:p></span></font></p>
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