[gmx-users] pull-code

lloyd riggs lloyd.riggs at gmx.ch
Fri Feb 17 18:44:48 CET 2012


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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