Project files provided as supporting information to the manuscript "Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model"

README file to the project files provided as supporting information to the manuscript "Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model"

October 8, 2024

Authors:
Giovanni Mattiotti, Manuel Micheloni, Lorenzo Petrolli, Lorenzo Rovigatti, Luca Tubiana, Samuela Pasquali, Raffaello Potestio

==================================

Trajectories and obsvervables relative to the scientific paper entitled:
"Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with oxRNA"

Authors:
Giovanni Mattiotti, Manuel Micheloni, Lorenzo Petrolli, Luca Tubiana, Samuela Pasquali, Raffaello Potestio

Brief description of the content of this folder:

|_ oxDNA-CCMV_force.zip: the modified version of the oxDNA software we used to make the simulations with the CCMV-like spherical potential described in the paper
|
|_ CCMV_RNA2_oxRNA_simulations
   |_ FOLDING (files of the "freely-folding" simulations)
   |   |_ FIRST_LAST_FRAMES (frames generated by oxDNA software)
   |   |   |_ 0.15M (first and last frames of the runs at 0.15M)
   |   |   |   |_ REP1 (files relative to REP1 / REPI)
   |   |   |   |   |_ first.dat
   |   |   |   |   |_ last.dat 
   |   |   |   |
   |   |   |   |_ REP2 (files relative to REP2 / REPII)
   |   |   |   |   |_ first.dat
   |   |   |   |   |_ last.dat 
   |   |   |   |
   |   |   |   |_ REP3 (files relative to REP3 / REPIII)
   |   |   |       |_ first.dat
   |   |   |       |_ last.dat 
   |   |   |
   |   |   |_ 0.50M (first and last frames of the runs at 0.50M)
   |   |   |  |_ [same structure as for 0.15M]
   |   |   |
   |   |   |_ 0.50M (first and last frames of the runs at 0.50M, T293K)
   |   |   |  |_ [same structure as for 0.15M]
   |   |   |
   |   |   |_ 0.50M (first and last frames of the runs at 0.50M, T293K, harmonic constraint to the ends)
   |   |      |_ [same structure as for 0.15M]
   |   |
   |   |
   |   |_ HB_FILES (base pairs files generated by oxDNA software)
   |   |   |_ hb_015M_I.dat    (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.15M salt concentration)
   |   |   |_ hb_015M_II.dat    (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.15M salt concentration)
   |   |   |_ hb_015M_III.dat    (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.15M salt concentration)
   |   |   |_ hb_050M_I.dat    (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.5M salt concentration)
   |   |   |_ hb_050M_II.dat    (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.5M salt concentration)
   |   |   |_ hb_050M_III.dat    (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.5M salt concentration)
   |   |   |_ hb_050M_293K_I.dat    (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.5M salt concentration, T 293K)
   |   |   |_ hb_050M_293K_II.dat    (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.5M salt concentration, T 293K)
   |   |   |_ hb_050M_293K_III.dat    (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.5M salt concentration, T 293K)
   |   |   |_ hb_050M_293K_harm_I.dat    (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.5M salt concentration, T 293K, harmonic constraint to the ends)
   |   |   |_ hb_050M_293K_harm_II.dat    (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.5M salt concentration, T 293K, harmonic constraint to the ends)
   |   |   |_ hb_050M_293K_harm_III.dat    (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.5M salt concentration, T 293K, harmonic constraint to the ends)
   |   |
   |   |_ example_input.ox (example of oxDNA input file used to launch simulations and dump observables and trajectories)
   |   |
   |   |_ example_input_harm.ox (example of oxDNA input file used to launch simulations with harmonic constraint to the ends and dump observables and trajectories)
   |   |
   |   |_ harmonic_ends.dat (constraint force file used to run simulations with harmonic constraint to the ends)
   |
   |_ PACKED
       |_ SIM_VTHEO (files of the simulations with the analytic-based external potential, as described in the paper...)
       |   |_ 0.15M (... with a salt concentration of 0.15M)
       |   |   |_ REP1 (Replica with id 1, or I)
       |   |   |   |_ MD_scripts (files required by oxDNA software to launch the simulation for this replica)
       |   |   |   |   |_ input_0.15M_REP1.ox (input file of oxDNA software to launch the simulation)
       |   |   |   |   |_ force_0.15M_REP1.dat (additional file required for the application of an external force in the simulation, containing the relative parameters)
       |   |   |   |
       |   |   |   |_ input_structure (structure files in oxDNA format, one of which is used as starting configuration for the specific replica)
       |   |   |   |   |_ PackingRNA2_0.15M_REP1.dat (last structure of simulation with time-dependent external packaging force)
       |   |   |   |   |_ PackingRNA2_0.15M_REP2.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)
       |   |   |   |   |_ PackingRNA2_0.15M_REP3.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)
       |   |   |   |   |_ PackingRNA2_0.5M_REP1.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)
       |   |   |   |   |_ PackingRNA2_0.5M_REP2.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)
       |   |   |   |   |_ PackingRNA2_0.5M_REP3.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)
       |   |   |   |
       |   |   |   |_ data (output data generated by the simulation)
       |   |   |       |_ 1.E (files of the observables dumped during simulation)
       |   |   |       |   |_ E_RNA2_0.15M_REP1.dat  (energies of the system per each time frame: time frame, potential energy U, kinetic energy, total energy)
       |   |   |       |   |_ P_RNA2_0.15M_REP1.dat  (internal pressure of the system: time frame, total pressure, stress tensor components xx, yy, zz, xy, xz, yz)
       |   |   |       |   |_ F_RNA2_0.15M_REP1.dat  (components of the external force acting on each nucleotide, ordered according to the topology, per each frame)
       |   |   |       |   |_ HB_RNA2_0.15M_REP1.dat (base pairs annotated, per each time frame dumped)
       |   |   |       |
       |   |   |       |_ 3.restart (restart/last configuration file dumped during simulation)
       |   |   |           |_ last_conf_RNA2_0.15M_Yukawa_REP1.dat (last frame dumped in the simulation, in oxDNA format)
       |   |   |
       |   |   |
       |   |   |_ REP2 (Replica with id 2, or II)
       |   |   |   |_ [same content as REP1, but relative to replica 2 or II]
       |   |   |
       |   |   |_ REP3 (Replica with id 3, or III)
       |   |       |_ [same content as REP1, but relative to replica 3 or III]
       |   |
       |   |_ 0.5M  (... with a salt concentration of 0.5M)
       |   |   |_ [same content as 0.15M, but for simulations done at 0.5M of salt concentration]
       |   |
       |   |_ 0.5M_293K_harm  (... with a salt concentration of 0.5M, Temperature 293K and harmonic constraint to the ends)
       |       |_ [same content as 0.15M, but for simulations done at 0.5M of salt concentration]
       |
       |_ SIM_VCCMV (files of the simulations with the structure-based external potential, as described in the paper)
           |_ [same content as SIM_VTHEO, but for simulations done with the structure-based external potential]

For any additional file or data not present here, that was used to produce results in the paper, please ask to: giovanni.mattiotti@inserm.fr, manuel.micheloni@unitn.it, lorenzo.petrolli@unitn.it