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On 14/11/2011 5:46 PM, Kei Sit wrote:
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<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><br>
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<br>
What does gmxcheck have to say about your trajectory files?<br>
<br>
Mark<br>
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