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<p class=MsoNormal><span style='color:#1F497D'>Hi Mark,<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>I ran gmxcheck and it returned
the following output:<br>
<br>
Checking file 1-21.trr<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>trn version: GMX_trn_file
(single precision)<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Reading
frame 0 time
0.000 <o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'># Atoms 7764<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Reading frame 49000
time 4900.000 <o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Item
#frames Timestep (ps)<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Step
49984 0.1<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Time
49984 0.1<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Lambda
49984 0.1<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Coords
49984 0.1<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Velocities
0<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Forces
0<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Box
49984 0.1<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>I understand now why the time is
10 times smaller in my analysis, but this now raises another question as to why
it is 0.1ps per frame. Would it have something to do with the converting from a
DCD format to a TRR format? I just checked the configuration file for my MD run
and I can still see that I’m running the simulation of 2fs timesteps and
saving output every 500 steps which should equate to 1ps. Once again, thank you
for your time in helping.<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Regards,<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'>Kei<o:p></o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";color:windowtext'>From:</span></b><span lang=EN-US
style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Mark Abraham<br>
<b>Sent:</b> Monday, 14 November 2011 6:47 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] Time unit issue with g_anaeig<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>On 14/11/2011 5:46 PM, Kei Sit wrote: <o:p></o:p></p>
<p class=MsoNormal>Hi all,<o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>I’m new to gromacs so I hope I haven’t done
something wrong that is extremely simple. I have recently been using gromacs to
analyse an MD trajectory using g_covar and g_anaeig. I have output saved to the
trajectory every ps and I currently have a trajectory with 49000 frames (49ns).
<o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>I initiate g_anaeig with this command:<br>
<br>
g_anaeig –v eigenvec.trr –f 1-21.trr –s protein.pdb
–eig eigenval.xvg –proj projection.xvg –xvgr –first 1
–last 8<o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>While this is being executed I see this:<o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>Reading frame 1000 time 100.00 <o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>which continues increasing as more frames are read.<o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>When I go to visualise projection.xvg, the time scale is in
ps (natural as the default value is in ps) but it only shows 4900ps and not
49000ps. <o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>My issue is this, why is the time constantly 10 times
smaller than the number of frames that are being read? Am I not entering
something correctly which fixes this? <o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><br>
What does gmxcheck have to say about your trajectory files?<br>
<br>
Mark<o:p></o:p></span></p>
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