[gmx-users] Time unit issue with g_anaeig

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 14 09:46:49 CET 2011

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?

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