# [gmx-users] pull-code

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Feb 17 18:03:52 CET 2012

```Hi Thomas

A few points below under your points

Thomas Schlesier wrote:
> Yes you are right, should be between 0 and >0.
>
> Do you have a window for a distance equal 0?
Yes
>
>
> This window should behave similar to the RDF-analysis. Because there
> are "no directions".

It doesn't. By this I mean the zero point of the reaction coordinate
does not give  a free energy minimum (actually the minimum is shifted to
the right) whereas from the reversible work theorem it does.
>
> Or to reformulate the problem.
> We make an umbrella window for a distance of 1. If particle stays
> there everything is fine. If particle moves to 0, it should be also
> fine (particle sees a force of k*1). If paticle moves to -1, it should
> see a force of k*2, but instead, the distance is 0 -> no force.
I don't understand from "if particle moves ......"
> If you have the umbrella window centered at 0 this problem vansihes ->
> if particle move it sees always a force.
>
> But one thing gives me headaches. I don't have this problem in my
> pulling simulation, because the distance between my reference and
> pulled group can not become zero:
> But concerning the reaction coordinate it will have a similar flaw
> like the RDF i think: It doesn't matter in wish direction the particle
> moves (left or right) due to the distance we would always say it moves
> along the reaction coordinate. In reality it moves sometimes in the
> negative direction of the reaction coordinate, but we always say it's
> a positve distance -> so positive value on the reaction coordinate.
> For an isotropic system this would not matter, but for system which we
> have a anisotrop reaction coordinate it should matter.
My system is isotropic
>
>
> Greetings
> Thomas
>
>
>
> Am 17.02.2012 17:07, schrieb gmx-users-request at gromacs.org:
>> Hi Thomas Many thanks for the reply again. At larger distances the two
>> curves match up quite well. The curve from the reversible work theorem
>> is better behaved and smoother but this could be solely due to
>> statistics. I am slightly confused about your statement "If the small
>> circle moves between 0 and any value <0 everything should be fine." Do
>> you not mean 0 and any value >0 ? Cheers Gavin 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
>

```