vdssb_gromacs
Absolute Dissociation Free Energy calculations on HPCs: vDSSB tutorial for GROMACS users
This is a technical tutorial for the calculation of the absolute dissociation free energy between PF-07321332 and 3CLpro on high performing architectures using a nonequilibrium alchemical approach with the GROMACS code. The theoretical background of the methodology can be found here and here . The procedure is divided into six consecutive steps. The major massively parallel computational steps consist in the HREM simulations (Step 3) and in the fast switching alchemical simulations (Step 5). The Steps 1, 2 and 4 are fast preparatory automatized procedures for running the two major computational jobs on the HPC, Step 3 and Step 5. The last Step 6 is the automatized post-processing of the vDSSB data. Full output data for the application PF-07321332-3CLpro can be found on the Zenodo repository ( https://zenodo.org/record/5139374 ).
Step 1 : Docking (local)
Step 2 : Running HPC_drug for HREM set-up (local)
Step 3 : HREM simulations (HPC)
Step 4 : Selection of the (enhanced sampled) configurations (HPC)
Step 5 : Fast Switching Alchemical Simulations (HPC)
Step 6 : Calculation of dissociation free energy (HPC/local)
Marina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, Piero Procacci
Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
If you have any questions, please feel free to contact the authors.