On 14/11/2011 5:46 PM, Kei Sit wrote:
Hi all,
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).
I initiate g_anaeig with this command:
g_anaeig --v eigenvec.trr --f 1-21.trr --s protein.pdb --eig
eigenval.xvg --proj projection.xvg --xvgr --first 1 --last 8
While this is being executed I see this:
Reading frame 1000 time 100.00
which continues increasing as more frames are read.
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.
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?
What does gmxcheck have to say about your trajectory files?
Mark
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