READ ME File For 'Computer Simulations of Cell Penetrating Peptides'

Dataset DOI: 10.52.58/SOTON/D1749

License: CC BY

ReadMe Author: Lauren Marie Reid, University of Southampton ORCID https://orcid.org/0000-0001-8327-0927

This dataset supports the thesis entitled Computer Simulations of Cell Penetrating Peptides
AWARDED BY: Univeristy of Southampton
DATE OF AWARD: 2021

DESCRIPTION OF THE DATA

The dataset includes the base replica REST2 MD trajectories (stripped of solvent atoms), run files and cluster analysis output for Chapters 4 and 5 of the thesis.
It also includes run files, WHAM input files and trajectory analysis output from the peptide-membrane simulations presented in Chapter 6

This dataset contains:

Chapter_4_data.zip
        Chapter_4_data/<force_field>/<solvent>/
                                                PLP_<force_field>_<solvent>.xtc = equilibrated trajectory frames (solvent stripped)
                                                run<replica_ID>.tpr = run files for each replica
						combined_equil_diheds.dat = equilibrated dihedral trajectory for DASH analysis
                                                combined_equil_dash.dat = DASH clustering output
                                                _clust_<clust_id>.pdb = cluster representatives
Chapter_5_TP2_data.zip
        Chapter_5_TP2_data/<force_field>/<solvent>/
                                                TP2_<force_field>_<solvent>.xtc = equilibrated trajectory frames (solvent stripped)
                                                run<replica_ID>.tpr = run files for each replica
						combined_equil_diheds.dat = equilibrated dihedral trajectory for DASH analysis
                                                combined_equil_dash.dat = DASH clustering output
                                                _clust_<clust_id>.pdb = cluster representatives
Chapter_5_ONEG_data.zip
        Chapter_5_ONEG_data/<force_field>/<solvent>/
                                                ONEG_<force_field>_<solvent>.xtc = equilibrated trajectory frames (solvent stripped)
                                                run<replica_ID>.tpr = run files for each replica
						combined_equil_diheds.dat = equilibrated dihedral trajectory for DASH analysis
                                                combined_equil_dash.dat = DASH clustering output
                                                _clust_<clust_id>.pdb = cluster representatives

Chapter_6_unbiased_sim_data.zip
        Chapter_6_unbiased_sim_data/<peptide>/<cap>/<repeat>/
                                         		run_peptide.xtc = peptide trajectory (solvent and POPC stripped)
                                                        run_paxis1.xvg = first principle of inertia of peptide helix trajectory
                                                        run.tpr = gromacs run file
							run.gro = output coordinate file (full system)
                                                        <residue>-POPC_dens.xvg = gromacs density analysis output for each residue, full peptide, P atoms and water
                                                        <peptide>-POPC_dist.xvg = distance between peptide and bilayer COMs trajectory
                                                        <leaflet>_P-POPC_dist.xvg = upper or lower leaflet P atom COM distance to bilayer COM trajectory
                                                        ave_com_<leaflet>_<property>_grid.txt = matrix style output of average local bilayer leaflet properties

Chapter_6_self_assembly_data.zip
	Chapter_6_self_assembly_data/<peptide>/<cap>/<initial_conf>/<repeat>/
							run_2_peptide.xtc = conventional MD peptide trajectory (solvent and POPC stripped)
							run_2_paxis1.xvg = first principle of inertia of peptide helix trajectory
							run.tpr = gromacs run file for self assembly
                                                        run_anneal.tpr = gromacs run file for annealing
                                                        run_2.tpr = gromacs run file for conventional MD 
							run_2.gro = output coordinate file (full system)
							<residue>-POPC_dens.xvg = gromacs density analysis output for each residue, full peptide, P atoms and water
                                                        <peptide>-POPC_dist.xvg = distance between peptide and bilayer COMs trajectory
                                                        <leaflet>_P-POPC_dist.xvg = upper or lower leaflet P atom COM distance to bilayer COM trajectory
							ave_com_<leaflet>_<property>_grid.txt = matrix style output of average local bilayer leaflet properties

Chapter_6_US_TP2_Amide_Cap_9_res_helix.zip
	Chapter_6_US_TP2_Amide_Cap_9_res_helix/<initial_position>/
							umbrella<window>.tpr = US window gromacs run file
							pullf-umbrella<window>.xvg = US window umbrella force trajectoy file
							<leaflet>_<position_label>/
										<residue>-POPC_dens.xvg = gromacs density analysis output
										ave_com_<leaflet>_<property>_grid.txt = matrix style output of average local bilayer leaflet properties
										umbrella<window>.gro = output coordinate file (full system)
Chapter_6_US_TP2_Amide_cap_8res_helix_and_random_coil.zip
	Chapter_6_US_TP2_Amide_cap_8res_helix_and_random_coil/<initial_conf>/<initial_position>/
							same file system as above

Chapter_6_US_TP2_NMe_cap.zip
	Chapter_6_US_TP2_NMe_cap/<initial_conf>/<initial_position>/
							same file system as above

Chapter_6_US_ONEG.zip
	Chapter_6_US_ONEG/<cap>/<initial_conf>/<initial_position>/
							same file system as above
										
							

Date of data collection: 1/10/2016 - 30/09/2020

Date that the file was created: March, 2021