[gmx-users] pull-code

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Feb 17 12:56:22 CET 2012

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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