From http://www.strodel.info/index_files/lecture/html/analysis-10.html
Biomolecular processes, such as folding or aggregation, can be described in terms of the molecule's free energy:
where kB is the Boltzmann constant, P is the probability distribution of the molecular system along some coordinate R, and Pmax denotes its maximum, which is substracted to ensure that δG = 0 for the lowest free energy minimum. Popular choices for R (so-called order parameters) are the RMSD, Rgyr, number of hydrogen bonds or native contacts, or principal components.
The free energy is typically plotted along two such order parameters, giving rise to a (reduced) free energy surface (FES).
Example: FES (in kcal/mol) for the aggregation of the GNNQQNY peptide forming a dimer in terms of Rgyr and the RMSD from a perfect parallel β-sheet
Generating FESs with generateFES.py
python generateFES.py -f rgyr_rmsd.dat -o rgyr_rmsd.png -t 300 -bx 100 -by 100 -lx Rgyr[nm] -ly RMSD[nm]
The resulting graphics can be viewed with okular:
okular FES.png
Instructions:
awk ' {if ( $1 !~ /[#@]/) print $2 } ' rgyr.xvg > rgyr.dat
awk ' {if ( $1 !~ /[#@]/) print $2 } ' rmsd_ca.xvg > rmsd_ca.dat
paste rgyr.dat rmsd_ca.dat > rgyr_rmsd.dat
python generateFES.py -f rgyr_rmsd.dat -o rgyr_rmsd.png -t 300 -bx 100 -by 100 -lx Rgyr[nm] -ly RMSD[nm]
awk ' {if ( ($1 > 0.77 ) && ($1 < 0.78 ) && ($2 > 0.75) && ($2 < 0.76)) print "Frame: ", NR-1,$1,$2}' rgyr_rmsd.dat > energy_min1.dat
gmx trjconv -f md_protein.xtc -s md_protein.tpr -o md_protein_EM1_fr1485.pdb -dump 7425
-dump
refers to a time, and not a frame. Thus, the time corresponding to the frame identified for a energy minimum has to be calculated. Let's assume we used a time step of 5 ps between the snapshots saved in the trajectory and that we identified frame 1485 representing the first energy minimum. We have thus obtained the corresponding time by multiplying the frame number with the time step (1485 * 5 ps = 7425 ps).VMD
).