parm noions.prmtop
trajin gamd2.nc
# Average the trajectory
rms first :1-1530&!@H=
average gaccAvg.rst7 restart
# Save coordinates in memory for further processing
createcrd crd1
run
# Read in average structure, tag as [avg]
reference gaccAvg.rst7.1 [avg]
# RMS-fit coordinates in crd1 to average
crdaction crd1 rms ref [avg] :1-1530&!@H=
# Calculate coordinate covariance matrix
crdaction crd1 matrix covar :1-1530&!@H= name gaccCovar
# Diagonalize coordinate covariance matrix for eigenmodes
runanalysis diagmatrix gaccCovar out evecs.dat vecs 2
nmwiz nmwizvecs 2 nmwizfile cas.nmd nmwizmask :1-1530&!@H=
# Now create separate PC projections for each trajectory
crdaction crd1 projection T1 modes evecs.dat beg 1 end 2000 :1-1530&!@H= \
 crdframes 1,50000 out T1.dat
crdaction crd1 projection T2 modes evecs.dat beg 1 end 2000 :1-1530&!@H= \
 crdframes 50001,100000 out T2.dat
crdaction crd1 projection T3 modes evecs.dat beg 1 end 2000 :1-1530&!@H= \
 crdframes 100001,150000 out T3.dat
crdaction crd1 projection T4 modes evecs.dat beg 1 end 2000 :1-1530&!@H= \
 crdframes 150001,200000 out T4.dat
crdaction crd1 projection T5 modes evecs.dat beg 1 end 2000 :1-1530&!@H= \
 crdframes 200001,250000 out T5.dat
# Calculate Kullback-Leibler Divergence vs time for PC histograms
# Trajectories 1 and 2, modes 1-5
kde T1:1 kldiv T2:1 klout KL-PC.agr bins 400 name AMD-MREMD-1
kde T1:2 kldiv T2:2 klout KL-PC.agr bins 400 name AMD-MREMD-2
kde T1:3 kldiv T2:3 klout KL-PC.agr bins 400 name AMD-MREMD-3
kde T1:4 kldiv T2:4 klout KL-PC.agr bins 400 name AMD-MREMD-4
kde T1:5 kldiv T2:5 klout KL-PC.agr bins 400 name AMD-MREMD-5
# This is repeated for trajectory pairs 3+4, 5+6, 7+8, and 9+10
# Calculate PC histogram with KDE, trajectory 1, mode 1
kde T1:1 out kde-PC.agr bins 400 name KDE1-1
# Calculate PC histogram, trajectory 1, mode 1
hist T1:1,*,*,*,200 out pca.hist.agr normint name HIST1-1
# Histogram calcs repeated for all trajectories+modes