Hi. I'm running the same TI calculations as in this paper Using AMBER18 for Relative Free Energy Calculations using the input files they provide here GitHub - linfranksong/Input_TI.The publication does mention that the CPU version of PMEMD was used for the NPT equilibration of the TI section (dual ligand system with timask and soft cores set up). I did try to run this step using the GPU version and although it does run, the ligands come out of the binding site.Was wondering why this step has to be run with the CPU version and if there is any way to run it on GPU instead.I was using Amber20. Perhaps Amber22 has solved this issue?Thanks,Bruno
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Received on Tue Dec 06 2022 - 05:30:02 PST
