PDZ3 domain, 1micro second simulation x 6 trajectories

PDZ3 domain (residues 306-415) in solution with a ligand peptide (KQTSV) and unbounded state. Initial structures : PDB 1BE9 and 1BEF A system of 8199 molecules (25461 atoms) was simulated. Virtual sites were used in some of the molecules. A total of 1000 ns were simulated with a time step of 4 fs.(HMR used) Neighbor searching was performed every 20 steps. The PME algorithm was used for electrostatic interactions. with a cut-off of 1.2 nm. A reciprocal grid of 56 x 56 x 56 cells was used with 4th order B-spline interpolation. A single cut-off of 1.273 nm was used for Van der Waals interactions. Pressure coupling was done with the Parrinello-Rahman algorithm. AMBER03 force field and TIP3P water model. Preparation and equilibration scripts were can be available as follws. https://github.com/fazzz/preparation_PDZ3 initial gro of production run: final_density_stabilization_holo.gro, final_density_stabilization_apo.gro topologies of production run: PDZ3_holo.top, PDZ3_apo.top MD input of production run: production.mdp job script:production_job.sh production tpr: production_holo.tpr, production_apo.tpr trajectories of production run: superimposed_1micros-10ns_holo_[A-C].xtc, superimposed_1micros-10ns_apo_[A-C].xtc animation: production_holo_A.mp4, production_apo_A.mp4