GridMol is a “one-stop” platform for molecular modeling, scientific computing and molecular visualization aided by High Performance Computing Environment. GridMol version 2.0 emphatically introduces two unique features, the first is fragment-based linear scaling quantum chemistry methods, such as molecular fractionation with conjugate caps and fragment molecular orbital methods; the second is visualization of computational processes, such as structural optimization and intrinsic reaction coordinate calculation. Compared with version 1.0, fragment-based linear scaling quantum chemistry methods implemented in GridMol version 2.0 can be used as a useful tool for performing quantum calculations for large molecular systems to explore the mechanisms involved in protein–ligand or targeted-drug interactions.