Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART)

Table 2 Overview of the PART performance benchmark showing the percentage of the total simulation time going to PART restraints as a function of different hardware architectures and different probe mixtures

	16 CPU cores	64 CPU cores	128 CPU cores	1 A100 GPU
Mix 1 PLUMED time (%)	13	22	36	71
Mix 2 PLUMED time (%)	3	6	22	43
Mix 3 PLUMED time (%)	5	12	28	50
Mix 4 PLUMED time (%)	8	12	28	62
Mix 5 PLUMED time (%)	12	21	36	66
Mix 6 PLUMED time (%)	4	10	26	50
Mix 7 PLUMED time (%)	10	18	34	68

Mix 1 is a copy of the Factor-Xa benchmark where all benzene atoms where used to calculate the COM. Mix 2 is the Factor-Xa system where the only cosolvent is propane at a concentration of 0.25 M and Mix 3 is a copy of Mix 2 but with a probe concentration of 0.5 M. Mix 4 is the Factor-Xa system where the only cosolvent is benzene at a concentration of 0.25 M. Mix 5 is a copy of Mix 4 but with a probe concentration of 0.5 M. In Mix 4 and Mix 5, the COM of benzenes was calculated using all benzene atoms. Mix 6 and Mix 7 are a copy of Mix 4 and Mix 5 respectively, but now calculating the COM using only the benzene carbon atoms

ISSN: 1758-2946