Analysis of MD trajectory using tSNE

Before starting anything with tSNE let’s read what is tSNE and how it has been compared with PCA. You can read it here. Several implementations of t-SNE are available here. A great introductory video on tSNE can be found here.

The dataset used in this explanation can be accessed here (named combine_times_ca.dcd and corresponding GRO file prot_ca.gro . Use VMD to open them and crosscheck).

# Download Matlab_r2017b

# Add the path of .dcd file reader for MatLab.Download the package from here

addpath('/home/sbhakat/matdcd-1.0')

# Give the path of your dcd file. In my case I am using a dcd file named combine_times_ca.dcd which has atoms starting from 1 to 331.

x=readdcd('/home/sbhakat/Plasmepsin_r1_r2_PCA/Gromacs_plmr2/Combine/combine_times_ca.dcd',1:331);

This will produce a following output

h =

struct with fields:

fid: 3
 endoffile: 42789396
 NSET: 10560
 ISTART: 0
 NSAVC: 1
 NAMNF: 0
 charmm: 1
 charmm_extrablock: 1
 charmm_4dims: 0
 DELTA: 1
 N: 331

# Perform Pincipal Component Analysis

[pc, score, latent, tsquare] = pca(x(2:end,:));

# Plot first two principal components

plot(score(:,1),score(:,2),'.')

# Label the plot

xlabel('PC1')
ylabel('PC2')

# It will pop up a window with PCA plot something the following

pca_combined

# Carrying on the calculation on the same Matlab window

rng default % for reproducibility

# Perform tSNE analysis with Barneshut algorithm

Y = tsne(x,'Algorithm','barneshut','NumPCAComponents',50);

#Produce the figure

figure
gscatter(Y(:,1),Y(:,2))
xlabel('tSNE1')
ylabel('tSNE2')

# It will produce something like the following

tsne_combined

Reference

The initial part of the tutorial was inspired by this one.

Collaboration on use of tSNE in molecular dynamics simulation is highly appreciated.