The directory "Research_Data" contains files to reproduce the enhanced-sampling simulations in "Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes"

There is one subdirectory (gzipped tarball) for each of the three tyrosines in solution ("water") or the crystal.
The file contents of the "crystal" and "water" subdirectories are the same for each residue, here for Y33 as an example:

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(y33-water.tar.gz)
Files	                    File types
......................................
y33.namd                    Input: NAMD configuration file

y33.0.restart.coor          Output: Cartesian coordinates for four different walkers
y33.1.restart.coor
y33.2.restart.coor
y33.3.restart.coor
	                
y33.0.restart.vel           Output: Velocities for four different walkers
y33.1.restart.vel
y33.2.restart.vel
y33.3.restart.vel 	
                    
y33.0.restart.xsc           Output: Cell dimensions for four different walkers
y33.1.restart.xsc
y33.2.restart.xsc
y33.3.restart.xsc 
                    
aqua.pdb                    Input: PDB file
	
aqua.psf 	                Input: Topology file
chi2.colvars 	            Input: Colvars configuration file (collective variable and free-energy method)

solvents/                   Input: Force-field parameter files for solvents
solvents/fb3_ions.str
solvents/fb4_ions.str
solvents/namdrc.fb3
solvents/namdrc.fb4
solvents/namdrc.opc
solvents/namdrc.spce
solvents/namdrc.spceb
solvents/namdrc.tip3p
solvents/namdrc.tip4pew
solvents/opc_ions.str
solvents/README
solvents/spceb_ions.str
solvents/spce_ions.str
solvents/tip3p_ions.str
solvents/tip4pew_ions.str 	

ff19SB/                     Input: Force-field parameter files for proteins
ff19SB/namdrc.ff19SB
ff19SB/README
ff19SB/parm19.prm
ff19SB/ff19SB.rtf
ff19SB/frcmod.ff19SB.prm 	

initial.0.restart.coor      Input: Cartesian coordinates for four different walkers
initial.1.restart.coor
initial.2.restart.coor
initial.3.restart.coor
	

initial.0.restart.vel       Input: Velocities for four different walkers
initial.1.restart.vel
initial.2.restart.vel
initial.3.restart.vel
	

initial.0.restart.xsc       Input: Cell dimensions for four different walkers
initial.1.restart.xsc
initial.2.restart.xsc
initial.3.restart.xsc 	

####################################################################################
(y33-crystal.tar.gz)
Files                       File types
......................................
y33.namd                    Input: NAMD configuration file
	
y33.0.restart.coor          Output: Cartesian coordinates for four different walkers
y33.1.restart.coor
y33.2.restart.coor
y33.3.restart.coor
	
y33.0.restart.vel           Output: Velocities for four different walkers
y33.1.restart.vel
y33.2.restart.vel
y33.3.restart.vel 	

y33.0.restart.xsc           Output: Cell dimensions for four different walkers
y33.1.restart.xsc
y33.2.restart.xsc
y33.3.restart.xsc 

crystal.pdb                 Input: PDB file
	

crystal.psf 	            Input: Topology file

y33-chi2.colvars 	        Input: Colvars configuration file (collective variable and free-energy method)

solvents/                   Input: Force-field parameter files for solvents
solvents/fb3_ions.str
solvents/fb4_ions.str
solvents/namdrc.fb3
solvents/namdrc.fb4
solvents/namdrc.opc
solvents/namdrc.spce
solvents/namdrc.spceb
solvents/namdrc.tip3p
solvents/namdrc.tip4pew
solvents/opc_ions.str
solvents/README
solvents/spceb_ions.str
solvents/spce_ions.str
solvents/tip3p_ions.str
solvents/tip4pew_ions.str 	

ff19SB/                     Input: Force-field parameter files for proteins
ff19SB/namdrc.ff19SB
ff19SB/README
ff19SB/parm19.prm
ff19SB/ff19SB.rtf
ff19SB/frcmod.ff19SB.prm 	

equilibrate.0.restart.coor  Input: Cartesian coordinates for four different walkers
equilibrate.1.restart.coor
equilibrate.2.restart.coor
equilibrate.3.restart.coor
	

equilibrate.0.restart.vel   Input: Velocities for four different walkers
equilibrate.1.restart.vel
equilibrate.2.restart.vel
equilibrate.3.restart.vel
	

equilibrate.0.restart.xsc   Input: Cell dimensions for four different walkers
equilibrate.1.restart.xsc
equilibrate.2.restart.xsc
equilibrate.3.restart.xsc