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<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Hello Gromacs users,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>I ran gmxcheck on a trr file I got from running energy minimization,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Gmxcheck’s output is:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>---------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Checking file 4PLMYWOrg01_em_tim.trr<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>trn version: GMX_trn_file
(single precision)<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><st1:City w:st="on"><st1:place w:st="on"><b><i><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial;font-weight:bold;
font-style:italic'>Reading</span></font></i></b></st1:place></st1:City><b><i><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial;font-weight:
bold;font-style:italic'> frame 0
time 0.000<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'># Atoms 55986<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Reading
frame 11 time 1001.000<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Timesteps at t=1000 don't
match (100, 1)<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Last
frame 11 time 1001.000<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'><o:p> </o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'><o:p> </o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Item #frames<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Step
12<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Time
12<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Lambda
12<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Coords
11<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Velocities
0<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>Forces
1<o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><st1:address w:st="on"><st1:Street w:st="on"><b><i><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial;font-weight:
bold;font-style:italic'>Box</span></font></i></b></st1:Street><b><i><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial;font-weight:
bold;font-style:italic'>
12</span></font></i></b></st1:address><b><i><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial;font-weight:bold;font-style:italic'><o:p></o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'><o:p> </o:p></span></font></i></b></p>
<p class=MsoNormal><b><i><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;font-weight:bold;font-style:italic'>gcq#259: "Everything
Must Go" (Red Hot Chili Peppers)</span></font></i></b><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'>------------------------------------------<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=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>So my question is – What does that mean “Timesteps
at t=1000 don’t match….”? <br>
(and where can I find more information regarding to gmxcheck messages?)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Thank you in advance,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Shay Amram<o:p></o:p></span></font></p>
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