MacroModel Reference Manual - ISP

Chapter 1: Capabilities and New Features1.2.7 Partition Coefficients• LOGP: A automated calculation method for estimating the logarithm of the partition coefficientfor a series of solutes between two immiscible liquids.1.2.8 Free-energy Perturbation• See the FEGA, FEIA, FEAV, FESA, and FESU commands; also the didactic write-up inChapter 15 of the MacroModel User Manual. Free-energy perturbation may be carriedout using mixed-mode Monte Carlo / Stochastic Dynamics, as well as SD or MD. Whenused in network-distributed mode, each process runs a separate window.1.2.9 Monte Carlo Simulation• Internal coordinate Metropolis Monte Carlo.• Structure sampling.• Evaluation of average enthalpy.• Mixed mode MD/MC simulations.• Importance sampling for MC and MD/MC.• A broad range of “smart” Monte Carlo and mixed MC/MD methods:Individual Methods:• SD: Stochastic Dynamics• ADF: All-Degree-of-Freedom Metropolis Monte Carlo• TMC: Torsional Monte Carlo• JBW: Jumping-Between-Wells importance sampling Monte CarloMixtures:• ADF/JBW• SD/TMC (original MCSD method)• SD/ADF• SD/JBW• SD/ADF/JBW1.3 Computational Features• Schrödinger products provide support for submitting jobs to batch queues. Any jobs thatcan be run on a remote machine can be submitted to a batch queue. See Chapter 6 of theInstallation Guide for information on setting up batch queue support.• MacroModel jobs can be run with a simplified input file that contains keyword-valuepairs. These jobs can be submitted with the $SCHRODINGER/macromodel command.MacroModel 9.7 Reference Manual 7