Preparing for FEP+ Jobs

Preparation for an FEP+ job is an important task. The choice of the system and the experimental structures is critical to the success of the project, and there are a number of considerations for setting up the structures that should be taken into account. Preparation of the structures themselves is also important.

In addition to preparing the structures, estimating the resources required for the job may be important, particularly for large systems. For systems with more than 100,000 atoms for a solvated ligand/receptor complex, you may need to switch to using more than 1 GPU per subjob, even for newer graphics card models with more than 10 GB memory. There is a script that you can use to estimate the memory required for an FEP job—see fep_memory_estimation.py Command Help for more information. You can estimate the number of atoms by building the initial system, including solvent, in the System Builder Panel. With a solvent buffer of 8 Å, the output structure approximately provides an upper limit to the size of the FEP systems. This information is needed to estimate the memory required.

The topics listed below give some guidance in preparing for successful calculations: