# Hydrogen bond analysis with cpptraj # Load topology and trajectory parm trpzip2.ff10.tip3p.parm7 trajin trpzip2.unfold.nc # All solute-solute and solute-solvent hydrogen bonds + water bridges. hbond All out All.hbvtime.dat solventdonor :WAT solventacceptor :WAT@O \ avgout All.UU.avg.dat solvout All.UV.avg.dat bridgeout All.bridge.avg.dat # Backbone hydrogen bonds only. Save time series data. hbond Backbone :1-12@C,O,N,H avgout BB.avg.dat series uuseries bbhbond.gnu # Create file containing only number of solute-solute and solute-solvent # hydrogen bonds, and number of solute-solvent-solute bridges. create nhbvtime.agr All[UU] Backbone[UU] All[UV] All[Bridge] # Calculate RMSD to first frame. rms BBrmsd :1-12@C,CA,N out BBrmsd.agr # Run to actually find hydrogen bonds and generate data. run # Perform lifetime analysis on backbone hydrogen bonds lifetime Backbone[solutehb] out backbone.lifetime.dat runanalysis