A novel method, Cholesky decomposition with adaptive metric (CDAM), is applied to the two-electron integral calculations in the fragment molecular orbital (FMO) method. We thus accelerate the Hartree-Fock and the second-order Moller-Plesset perturbation (MP2) energy calculations substantially. Especially, the MP2 part for fragment dimers, which is computationally expensive, is accelerated by a factor of about 10. The CDAM approximations would enable FMO-MP2 calculations to easily process multiple structure samples even including dynamics of large molecular systems and lead to next-generation high-performance computations where statistical samplings or free energy estimates would be important. (C) 2010 Elsevier B.V. All rights reserved.