Conformational Plasticity of β-rich Proteins: Molecular Insights into Stability, Dynamics, and Functional Adaptation of Bet v 1-like Proteins

The zip files contain data related to individual molecular dynamics simulations. The contents of each archive are as follows:

*archive*.pdb -> Initial Structure
*archive*_solv.pdb -> Start Structure (Solvated) 
*archive*.prmtop -> Initial Topology *archive*.inpcrd -> Initial Velocities
*archive*.mdcrd -> Representative Trajectory File Min.in -> Input for First Minimization Min-II.in -> Input for Seccond Minimization

stage1_heat_5_50K_for_10ps.in -> Input for Heating from 5K to 50K in 10 ps
stage1.rst -> Restart Heating from 5K to 50K in 10 ps
stage1.out -> Log for Heating from 5K to 50K in 10 ps
stage1.mdcrd -> Trajectory of Heating from 5K to 50K in 10 ps

stage1_equil_50K_for_100ps.in -> Equilibration in 50K for 100 ps
stage2.rst -> Restart Equilibration in 50K for 100 ps
stage2.out -> Log for Equilibration in 50K for 100 ps
stage2.mdcrd -> Trajectory of Equilibration in 50K for 100 ps

stage2_heat_50_100K_for_10ps.in -> Input for Heating from 50K to 100K in 10 ps
stage3.rst -> Restart Heating from 50K to 100K in 10 ps
stage3.out -> Log for Heating from 50K to 100K in 10 ps
stage3.mdcrd -> Trajectory of Heating from 50K to 100K in 10 ps

stage2_equil_100K_for_100ps.in -> Input for Equilibration in 100K for 100 ps
stage4.rst -> Restart Equilibration in 100K for 100 ps
stage4.out -> Log for Equilibration in 100K for 100 ps
stage4.mdcrd -> Trajectory of Equilibration in 100K for 100 ps

stage3_heat_100_150K_for_10ps.in -> Input for Heating from 100K to 150K in 10 ps
stage5.rst -> Restart Heating from 50K to 100K in 10 ps
stage5.out -> Log for Heating from 50K to 100K in 10 ps
stage5.mdcrd -> Trajectory of Heating from 50K to 100K in 10 ps

stage3_equil_150K_for_100ps.in -> Input for Equilibration in 150K for 100 ps
stage6.rst -> Restart Equilibration in 150K for 100 ps
stage6.out -> Log for Equilibration in 150K for 100 ps
stage6.mdcrd -> Trajectory of Equilibration in 150K for 100 ps

stage4_heat_150_200K_for_10ps.in -> Input for Heating from 150K to 200K in 10 ps
stage7.rst -> Restart Heating from 150K to 200K in 10 ps
stage7.out -> Log for Heating from 150K to 200K in 10 ps
stage7.mdcrd -> Trajectory of Heating from 150K to 200K in 10 ps

stage4_equil_200K_for_100ps.in -> Input for Equilibration in 200K for 100 ps
stage8.rst -> Restart Equilibration in 200K for 100 ps
stage8.out -> Log for Equilibration in 200K for 100 ps
stage8.mdcrd -> Trajectory of Equilibration in 200K for 100 ps

stage5_heat_200_250K_for_10ps.in -> Input for Heating from 200K to 250K in 10 ps
stage9.rst -> Restart Heating from 200K to 250K in 10 ps
stage9.out -> Log for Heating from 200K to 250K in 10 ps
stage9.mdcrd -> Trajectory of Heating from 200K to 250K in 10 ps

stage5_equil_250K_for_100ps.in -> Input for Equilibration in 250K for 100 ps
stage10.rst -> Restart Equilibration in 250K for 100 ps
stage10.out -> Log for Equilibration in 250K for 100 ps
stage10.mdcrd -> Trajectory of Equilibration in 250K for 100 ps

stage6_heat_250_300K_for_10ps.in -> Input for Heating from 250K to 300K in 10 ps
stage11.rst -> Restart Heating from 250K to 300K in 10 ps
stage11.out -> Log for Heating from 250K to 300K in 10 ps
stage11.mdcrd -> Trajectory of Heating from 250K to 300K in 10 ps

stage6_equil_300K_for_5000ps.in -> Input for Equilibration in 300K for 5000 ps
stage12.rst -> Restart Equilibration in 300K for 5000 ps
stage12.out -> Log for Equilibration in 300K for 5000 ps
stage12.mdcrd -> Trajectory of Equilibration in 300K for 5000 ps

Prod.in -> Input for Step for Production (2 ns)