[gmx-users] Force output from Distance Constraint on pair of Cations

[Joshua D Monk]

Hello everyone.  I have seen a lot of post for the PULL function in Gromacs 4.0.  ( I am using Gromacs 4.0.3)

I have also been trying to use this function and I had a question about the Force output.

 

The system I am working with is a pair of Ionic Liquids in spc216 solution.

 

I want to find the Average Force at different distances for the Cation of the Ionic Liquid to find the PMF.

Therefore I define the COM of Cation 1  as the reference.

And I restrain pull_group1 and pull_group2.

 

 

Using a program I have placed the Cations at specific distances from each other.  In this case they should be 1.0 nm  from one another.  Therefore the pull_init1 and pull_init2   are 1.006 and 1.109 which are distances given when I create the TPR.

 

When I run this simulation I get the Force file  Constrain.Beti.H10_4F.xvg

My question is about the Force file.

 

I understand that it gives the Force along the Z direction that will keep the Cations a distance of 1.0 nm from one another as defined.  However when I plot these values in the Force output I get an average of ~0   since there are both +Forces and -Forces.

 

It makes sense to me how these forces are both positive and negative, but I am not sure how to use these values for analysis is the equation:

 

 

W(D) = ∫<f(D’)> dD’

 

Where W(D)  is the PMF. D is the reaction coordinate, and F(D) is the force required to constrain the reaction coordinate.

 

Since it calls for the average of the forces should I take the Absolute Value of these Forces to get the magnitude because they are direction dependant?

 

Joshua Monk

 

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