[gmx-users] tutorial umbrella sampling

Matthias Kiesel matze.kiesel at gmail.com
Fri Nov 27 23:36:29 CET 2015

Hi All,

I am currently doing the umbrella sampling tutorial by Justin Lemkul, 
but i have a problem with creating the right configurations for the 
umbrella sampling run. After running the first pull simulation and the 
given perl script the com distances don´t go from 0.5nm to 5nm, instead 
they start at 0nm, go negative for a some time grow until ~0.3nm and go 
back to small and negative values again.
When I visualize some of the .gro files (like conf250.gro) I can see 
something being pulled away from the rest of the Protein (how can I 
verify its Chain_A?) and in the created pullx.xvg the desired a 
COM-Distance curve going from 0.5nm to ~5nm is shown. Thats why i 
thought it´s a issue with the perl script or the trjconv / distance 
commands so that the wrong distances are extracted from the 
trajectories, but i couldn´t resolve it. I used the following trjconv  
command and the provided provided perl script:

gmx trjconv -s pull.tpr -f traj_comp.xtc -o configs/conf.gro -sep // There was not traj.xtc file, only a traj_comp.xtc, any explanations?

I did the rest of the tutorial as suggested. I hope someone is nice enough to give me a hint to a solution :)


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