[gmx-users] pull-code

Thomas Schlesier schlesi at uni-mainz.de
Fri Feb 17 16:34:22 CET 2012

Hi Gavin,
if i remember correctly it was a system about pulling a ligand from a 
binding pocket?
To make the system simpler we have a big circle and in the middle a 
small circle. And we assume that the potential minimum for the 
interaction between both circles is when the small cirlce is in the 
middle of the large circle.
Now we do the Umbrella sampling. For a window which is centered at a 
distance which is sligthly greater then 0, we will get problems. Assume 
small circle is sligthly shifted to the right. And the other windows are 
also in this dircetion. (-> reaction coordinate goes from zero to the 
right dircetion)
If the small circle moves between 0 and any value <0 everythig should be 
fine. But if the small circle moves to the left, we will also get a 
positive distance. Problem is from the above defined reaction coordinate 
it should be a negative distance. So we are counting the positive 
distances too much.
To check this, you could use *g_dist* to calculate the distance for both 
molecules for the problematic windows. Then project the resulting vector 
onto your reaction coordinate. Then you should see the crossings between 
the right and left side.

How do the two free energy curves compare for larger distances, where 
you can be sure, that you do not have this 'crossing problem'?



Hi all

I am returning to a query I had a few weeks ago regarding a discrepancy
between two free energy curves. One calculated using umbrella sampling,
the other calculated via the reversible work theorem from the RDF. There
is sufficient sampling of the dynamics in the RDF so this method is viable.
Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y.
The free energy curve from the pull-code method does not give me a
minimum at the zero value of the order parameter whereas the RDF method
does. Someone said before about double counting of positive distances at
small values of the order parameter and therefore information is lost at
very small distances.

Is this correct?
I am slightly concerned that my curves are not giving me the correct
information involving a very important state in my reaction coordinate.

Also when this dist restraint (which cannot be negative) is implemented
are there issues with the normalisation of the histograms from g_wham?



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