[gmx-users] pull code with defined negative relative displacements

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Nov 15 23:11:43 CET 2009

Hi Berk,

I do not mean the box 0, and I am aware about the pull distance  
needing to be less than half of the smallest box length. Please allow  
me describe a bit more rigorously what I need to avoid. I will use an  
example that is totally fictitious, but is designed to emphasize the  
bimodal sampling issue that is relevant to my actual study.

1. Imagine that one wants to calculate the PMF for a water molecule  
along the normal to an asymmetric bilayer in which one leaflet is POPC  
and the other is lipidA.

2. The free energy for that water residing 0.1 nm away from the  
bilayer center in the POPC leaflet (call it -0.1 nm from the bilayer  
center) needs to be calculated separately from the free energy for  
that water residing 0.1 nm away from the bilayer center in the lipidA  
leaflet (call it +0.1 nm from the bilayer center).

3. Let the force constant be 500 kJ/mol/nm^2 and let the user apply  
pull_geometry=distance and pull_init1=0.1 while starting the replica  
at 0.1 nm from the bilayer center in two simulations where one takes  
(a) a starting water position that is 0.1 nm toward the POPC  
headgroups and the other takes (b) a starting position of the water to  
be 0.1 nm toward the lipidA headgroups.

4. I posit that the probability distributions of the water about the  
bilayer normal from simulations (a) and (b) in part 3 above will  
converge to the same distribution and that this distribution will be  
bimodal with one peak at -0.1 nm and one peak at +0.1 nm. This is  
because the simulation that started at -0.1 (0.1 nm closer to the POPC  
headgroups) will, even under the biasing force, infrequently cross the  
bilayer center of mass and then be closer to the lipidA heagroups. At  
this point. the direction of the applied force will the change to draw  
the water toward the other possible location at +0.1 nm.

5a. For displacements >> 0.1 nm, this will not be a problem.
5b. For larger force constants, this will not be a problem at 0.1 nm,  
but will still be a problem for some closer centers of restraint.

6. pull_geometry=distance is entirely incompatible with this approach.

7. pull_geometry=position does appear to work.

Thanks for your patience,

-- original message --


Sorry, but I have no clue what you mean with sampling >0
and how you would end up with a bimodal distribution.

You don't mean the box 0, do you?
That is irrelevant.
What can be a problem is that you pull distance should not be more  
than half the box length.


> Date: Sun, 15 Nov 2009 12:33:30 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> > I only now noticed Justin mail on g_wham.
> > You can probably also use pull_geometry=distance and pull_init=1,
> > if you starting structure has group1 close to 1 nm below group 0.
> Agreed, although this will not work when the force constant is not   
> strong enough to inhibit any sampling >0 -- wherein the distribution  
>  about 0 would become bimodal and this is something that I can not  
> allow.
> As far as I can tell, pull_geometry=position, pull_init1<0, and   
> pull_vec1=0 0 0 is the solution, as per my previous message.
> Thank you,
> Chris.

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