In the top-level directory, there are two input files for CHARMM: (1) orderparams.inp -> to calculate quantities for a given structure used to obtain the structural order parameters (2) charmm_md.inp -> to run molecular dynamics simulations in two parts: an initial heating phase (commands commented out) and a constant-temperature production phase

The four subdirectories alpha0/ alpha0.3/ alpha0.5/ and alpha0.7/ contain input and output files for the kinetic transition networks assembled using discrete path sampling for the four different overall potentials. These directories contain: (1) min.data -> database of minima in the kinetic transition network (2) ts.data -> database of transition states in the kinetic transition network (3) points.min -> coordinates of the minima in min.data (direct access, unformatted file) (4) points.ts -> coordinates of the transition states in ts.data (direct access, unformatted file) (5) min.A, min.B -> input files for PATHSAMPLE required for certain types of run (6) pathdata -> input file for the PATHSAMPLE program for discrete path sampling (7) odata.connect -> input file for running double-ended connections using the OPTIM program with CHARMM interfaced (8) 1le0_extended.pdb -> PDB file for an extended structure of the trpzip1 peptide, used as input to CHARMM and OPTIM with CHARMM interfaced (9) perm.allow -> input file used by OPTIM and PATHSAMPLE for the optimal alignment of pairs of structures with respect to overall translation, rotation and permutational isomerization (10) input.crd -> template input coordinates file based on CHARMM card format* (11) chemshifts.dat -> input file for OPTIM, containing the reference CamShift chemical shifts (NOT needed for forcefield only calculations, i.e. directory alpha0/) (12) dinfo -> input file for plotting disconnectivity graphs using the disconnectionDPS program Subdirectory basinhopping/ (1) data -> input file for the GMIN program with CHARMM interfaced, to show the options used (2) [1,2,3,4,5,6,7,8,9,10].dbase.1 -> output coordinate files, based on CHARMM card format*, containing the lowest-energy minimum found by GMIN in the 10 independent runs starting from different configurations (labelled by the run number) Running PATHSAMPLE with the current keywords will compute the "fastest" path through the network between the minima whose indices are specified in the min.A and min.B files, at 298K. The binary files can be read using the PATHSAMPLE program compiled with the NAG Fortran Compiler Release 6.0 (64 bit). * Input and output CHARMM coordinate files are formatted based on the CHARMM card format, for free-field reading, but with modifications to the source code to allow greater precision in the coordinates and longer line lengths (120 characters), found to be essential to our work.

For the meaning and operation of specific keywords in the input files please refer to the user manuals (see http://www-wales.ch.cam.ac.uk/software.html and http://www.charmm.org/documentation/chmdoc.html). For further enquiries please email Prof. David J. Wales dw34@cam.ac.uk.