Formatting changes

running-path

@@ -0,0 +1,74 @@
+The PATH program can be run using the command
+
+path.py -h
+
+This gives a list of all the flags for customizing the simulation.
+
+The program can be used in two different modes - "path" and "rock" mode. "path" mode calculates the most probable pathways between two equilibrium states of a protein. "rock" mode calculates the trajectory of a single structure along its nth vibrational mode. The default mode is "path" which can be changed to "rock" using the '-ty' flag. Further customization options with each mode is described below.
+
+#####################
+    "path" mode:
+#####################
+
+The most probable pathway between two equilibrium states of a protein can be calculated used the following command.
+
+path.py -f1 <start structure> -f2 <end structure>
+
+The two structures are PDB files. To successfully calculate the conformational change trajectories using the PATH program, the number of atoms in both the structures must be the same and so should the order of atoms in both the files.
+
+The program outputs the transition state (trans.pdb) and the trajectory (traj.pdb) connecting the two end states. Both these files are in the PDB format. It also outputs the energy (engy) of each structure along the trajectory relative to the two end states.
+
+The program also generates an output parameter file (path_log) which contains the RMSD between the two states of the protein, the difference in energy between the two minima, based on the "path" potential (described below), the time to the transition state from the starting structure (tbar left), time to the final state from the transition state (tbar right) and the energy of the transition state relative to the final state (Utrans).
+
+-n flag:
+
+The number of structures in the trajectory that the program outputs can be specified using the '-n' flag in the above command in the following way 
+
+path.py -f1 <start structure> -f2 <end structure> -n 11
+
+This commands outputs a trajectory with 11 structures, which includes the two end states as well.
+
+-ca flag:
+
+By default, the above commands performs an all atom simulation. But, it is also possible to run an all atom simulation or a C-alpha only simulation using the '-ca' flag.
+
+path.py -f1 <start structure> -f2 <end structure> -ca 1
+
+This command performs a C-alpha only simulation.
+
+As PATH builds a Hessian matrix for both the structures which is later diagonalized for calculating the trajectory, the size of the protein determines how long it takes it calculate the trajectory. An all atom simulation of proteins which have less than 1000 atoms can be run on Desktop computers (8 GB RAM with i5 processor). For large systems, it is recommended to run PATH calculations on computers with larger memory. If only the overall dynamics of the protein is of interest then an alternative method to simulate large proteins is to run C-alpha only simulations. We have observed that the C-alpha only simulation can reproduce most of the essential dynamic information about the trajectory that an all atom simulation generates.
+
+
+#####################
+    "rock" mode:
+#####################
+
+This mode of the program calculates the trajectory along the nth vibrational mode of a single structure. It can be run using the command
+
+path.py -f1 <structure> -ty rock
+
+Apart from the '-n' and '-ca' flags that behave in the same manner as in the "path" mode, there are several additions flags that could be used with the "rock" mode.
+
+-m flag:
+
+This flag can be used to specify the nth vibrational mode along which the rocking trajectory is calculated. By default the first vibrational mode is used.
+
+-exag flag:
+
+Often the magnitude of displacement along the nth vibrational mode is small and may require an increase in the magnitude to make the displacement more perceptible. This flag can use used to specify a factor that is then multiplied to the displacement. The default value is 10.
+
+-c flag:
+
+Constraints can be applied between CA atoms of pairs of aminoacids by inputting a constraints file using the '-c' flag. The constraints file consists three columns - the first column specifies the magnitude of the constraints relative to the regular force constants, and the other two columns specify the aminoacid pairs that are constrained. For example the constraint files can consist of the following lines
+
+10 A37 A43
+100 A57 B74
+
+The first line constrains the CA atoms of aminoacids 37 and 43 in chain A with a force constant of magnitude 10 times greater than the regular force constants.The second line constraints CA atoms of aminoacid 57 in chain A to aminoacid 74 in chain B with a force constant 100 times greater than the regular force constants.
+
+#####################
+  "path" potential:
+#####################
+
+For all atom simulations, the program uses the ANM potential energy function described in the Chandrasekaran et al. paper (doi: 10.1063/1.4941599). For CA only simulations, the program uses a mass weighted version of the empirical potential described in the Hinsen et al. paper (doi: 10.1016/S0301-0104(00)00222-6)
+