[gmx-users] pull-code

Thomas Schlesier schlesi at uni-mainz.de
Fri Feb 17 19:01:27 CET 2012

Yes, the pulling is in all direction. But i tried to explain it in one 
Lol, send last mail only to Gavin.

The real problem (i think) is the following:
We have our pulled group  1nm right from the reference group, and the 
umbrella potential is also centered the (we used pull_start=yes, or 
The umbrella force is zero.

Now we move the particle 2nm to the left, to we have the same distance, 
but into the left direction. Since the distance is the same, the 
umbrella force is zero. On its way the umbrella force increases, maximum 
when the pulled group is on top of the reference group, and then 
decreases back to zero.
But we wanted a potential, where it doesn't matter if the particle moves 
to the left or right, force should always increase. But with 
pull_geometry=distance we can't get it.
If the distances between reference and pulled group are big enough we 
don't run into this problem.



I was following your argument but then doesnt pull_dim=Y Y Y mean it 
pulls in all directions at once?  I use pull_dim=N N Y , or just 1 pull 
direction and it works.  I might be wrong, but would be interesting if 
you got it to work like that for a small molecule.

Stephan Watkins

-------- Original-Nachricht --------
 > Datum: Fri, 17 Feb 2012 16:34:22 +0100
 > Von: Thomas Schlesier <schlesi at uni-mainz.de>
 > An: gmx-users at gromacs.org
 > Betreff: [gmx-users] pull-code

 > 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'?
 > Greetings
 > Thomas
 > 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?
 > Cheers
 > Gavin
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