OTF string method: use 2 COMs for the ligand.

^{1.- Overview}

In this brief report we calculate the first convergence test on a modification of the OTF string method that uses 2 centers of mass (COMs) as CVs to monitor the binding of the ligand DIH to the protein PNP.

^{2.- Selection of the new CVs}

The new CVs are the centers of mass of the heavy atoms from the two ring systems in the ligand DIH. More clearly in the next figure we show (in yelow) the precise location of these COMs.

^{3.- COM Positions at convergence}

In the next plot I used a function to plot in two different colors the positions of the COMs along the curve (up to the final iteration so far). Notice that the COMs describe a complex dynamics which seems to correspond the the motions of the ligand using just one COM. However, additional calculations comparing 1COM and 2COM results need top be provided

library(knitr) #load the library to 'knit' a markdown doc in R.
library(rgl)   #load the 3D ploting library 'rgl' 
source("hooks-extra.R")  #source some extra functions to insert interactive 3d scenes in html 
knit_hooks$set(webgl = hook_webgl) #define the hooks

The strings data files in this new procedure are formed by 21 rows (images) and 6 columns (CVs). The first 3 are the COM coordinates for the first center and the last 3 columns are the COM coords for the second center.

#load the last OTF string and visualize dimensions of the data file for one string
lastS <- read.table("string450.dat")
dim(lastS)

## [1] 21  6

Now the plot of these 2 COMs along the last OTF string

source("myFunctions.R")
plot6D(lastS,"blue","red")

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^{4.- Convergence}

Now we plot the convergence of the procedure. The convergence is based on the distances between iterations in 6D dimensions.

#create a 'total' data frame with all the 450 strings comming from the iterations
df <- pasteDF2COM(450)  
plot(convDF(df),xlab="Iterations",ylab="Distance",main="Convergence plot")

^{5.- Partial conclusions}

This is, of course, a small convergence test. So far the algorithm seems to behave similarly to the 1 COM case. We now have a slighly more complicated system, but the convergence seems to arrive within 500 iterations. In a first approximation, the motions of the 2 COMs seems to describe a complex dynamic that intuitively agrees with the entry converged string that we observed for the 1 COM case although some additions tests are needed to confirm this statement.