[gmx-users] Time unit issue with g_anaeig

Kei Sit kei.sit at qut.edu.au
Mon Nov 14 07:46:22 CET 2011

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?

Any help would be greatly appreciated. Many thanks in advance!

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