This is a collection of scripts for running and analysing steered molecular dynamics constant velocity pulling on a set of PDB files.

The scripts included here have require VMD (Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.) 
namd2 is is also required for running the minimizations, equilibrations, and pulling molecular dynamics.

Files here are:
SMD.pl		|	This is the primary script for generating the namd conformation files for pulling of pdb files.  Also automates psf generation for most proteins, but examination of psf and pdb is recommended.

SMD.pm		|	This files contains the subroutines used in SMD.pl.  Must be in the same directory as SMD.pl

SMD_analysis.pl	|	This file can be used after the namd runs are completed.

The outputs of this script are .dat files:
<>_formated.dat :force/time data that has been translated for easy plotting
<>_smooth.dat :force/time data that has been smoothed by an averaging window to make the plots easier to read and analyse
Will also output a table of Models, GDT_TS values and BreakForce values


SMD_analysis.pm	|	This files contains the subroutines used in SMD_analysis.pl.  Must be in the same directory as SMD_analysis.pl


Scripts assume the directory structure

     |-pdb	# Folder for pdb and psf files
     |-perl	# Folder for *.pl and *.pm scripts
-SMD-|-conf	# Folder for conformation files (.conf)
     |-output	# Folder for output files (.coor .xsf .dcd .log ect.)
     |-models	# Folder for output files (par_all36_prot.prm and toppar_water_ions_namd.str)
     |-dat	# Folder for formated force data (.dat)


pdb files should be organized into target sets.
example:
/pdb/T0644/T0644TS123_1.pdb

Once pdb files are in their respective folders, run ./perl SMD.pl
This will make 5 .conf files for each pdb file.

minimize.conf		# Minimize energy to remove clashes
Equilibrate.conf	# Phase 1 of bringing simulation to running temp
Equilibrate_step2.conf	# Phase 2 of bringing simulation to running temp
pulled_c_v.conf		# Phase 1 of pulling model
pulled_c_v_step2.conf	# Phase 2 of pulling model

run these in the order above.  Each run requires the output files of the former.
can be run with namd2.

namd2 ./conf/<pdb>_minimize.conf > ./output/<pdb>_minimize.log
namd2 ./conf/<pdb>_Equilibrate.conf > ./output/<pdb>_Equilibrate.log (Crashing from Periodic Boundary Conditions is normal)
namd2 ./conf/<pdb>_Equilibrate_step2.conf > ./output/<pdb>_Equilibrate_step2.log
namd2 ./conf/<pdb>_pulled_c_v.conf > ./output/<pdb>_pulled_c_v.log (Crashing from Periodic Boundary Conditions is normal)
namd2 ./conf/<pdb>_pulled_c_v_step2.conf > ./output/<pdb>_pulled_c_v_step2.log

After these have finished, run SMD_analysis.pl.  This will generate force-time curves in /dat.
It will also print a table of:

PDB|GDT_TS|Break Force