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# Concerning files proteinG_trajectories.tgz:
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This directory contains the proteinG trajectory and topology files generated
from MD simulations.

1pgb_solv_ions.gro - The all-atom gromacs file
1pgb_solv_ions.pdb - The all-atom PDB file
1pgb_out.dcd - The all-atom trajectory

1pgb_stripped.pdb - A stripped PDB file - alpha carbons only
1pgb_stripped.dcd - A stripped DCD file - alpha carbons only

postsim.cpptraj - CPPTRAJ script to strip all-atom trajectory and structure files


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# Concerning files: 3W5A_apo.tgz, 3W5A_ATP.tgz, and 3W5A_dATP.tgz:
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Triplicate simulations are carried out for the 3W5A protein in the directories
The follow nucleotide counditions were simulated: 
- apo (no nucleotide bound, but with Mg2+)
- ATP and Mg2+
- deoxy-ATP and Mg2+ (dATP)

Each directory has a topology file (.parm7) and trajectory file .dcd. 
Additionally, there is a pdb file that can be used as the topology for the netsci analysis. 
Finally, there is an average structure for each of the simulation structures that is used in 
the netsci pathfinding analysis. 

The simulations were run using AMBER for 300 ns and steps saved every 5 ps, leading to 60000 frames. The 
first replicate was run for 312.25 ns and steps saved every 5 ps, for 62500 frames. 


Internal note:
The original replicated and storage numbering was 2-4 (and a 5th for ATP). These numbers were 
shifted to 1-3 and the original ATP rep3 simulation showed ATP leaving the pocket, and 
therefore a 5th trajectory was run to replace it. 

apo and dATP:
2->1
3->2
4->3
ATP:
2->1
5->2
4->3
3-> discarded