[gmx-users] pull-code

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Feb 17 17:19:10 CET 2012

Hi Thomas

I am sorry to bother you but if you could answer a few questions I have
about how the pull-code works with respect to my system I would really
appreciate it.
My system is a liquid and I am trying to pull one substituent of one
liquid molecule in a certain region of another liquid molecule using as
I said earlier pull_geometry =dist and pull_dim =YYY.
Also pull_start = no
Say I have a window with pull_init=0

1) At the very start of the simulation the pullcode calculates the
vector between the two groups? Is there anything particularly
significant about this initial vector? Is this distance vector
recalculated at every step?
2) Does it compare the distance vector an time t with that at time 0.?
3) Given the initial vector can this vector change (i.e. dierection) or
does the distance between the two groups vary only along this vector
(i.e. in a line) ?



Thomas Schlesier wrote:
> 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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