Non-zero Lennard-Jones parameters for the Toukan–Rahman water model: more accurate calculations of the solvation free energy of organic substances

To the fast calculation of the solvation free energy. Combining expanded ensembles with L2MC

“…For larger molecules even larger number of windows may be required. The proposed algorithm with 61–100 windows was recently used to calculate the distribution constants of drug candidates in the octanol/water system in the SAMPL6 competition 13 . Its effectiveness was sufficient to perform this work on personal desktop computers.…”

“…These methods are significantly more computer‐efficient than earlier ones, such as free energy perturbation (FEP), 6 thermodynamic integration (TI), 7,8 which, combined with the increased power of computers, made free energy calculations available even on personal computers. Expanded ensemble method showed its efficiency in computations of large free energy differences in a wide variety of cases, 9–15 and its detailed analysis and comparison with other methods were discussed in a number of reviews 16,17 …”

Exploration and validation of force field design protocols through QM-to-MM mapping

“…Different choices are made for example in the design of the TIP3P and CHARMM modified water model, 65 while there is precedent for improved agreement with liquid data using Lennard-Jones parameters on polar hydrogen atoms. 66 While separate mapping parameters have been previously proposed for polar and non-polar hydrogen atoms, the effect on accuracy has not been directly explored, 40 and so we add this comparison to our list of model protocols to be tested (Table 1, model 4a ).…”

“…An additional choice in force field design is whether to include Lennard-Jones parameters on polar hydrogen atoms, or to effec-tively redistribute them onto the neighbouring heavy atom 33 (see Supporting Information S1.3). Different choices are made for example in the design of the TIP3P and CHARMM modified water model 65 , while there is precedent for improved agreement with liquid data using Lennard-Jones parameters on polar hydrogen atoms 66 . While separate mapping parameters have been previously proposed for polar and non-polar hydrogen atoms, the effect on accuracy has not been directly explored 40 , and so we add this comparison to our list of model protocols to be tested (Table 1, model 4a).…”

One--Component Plasma of a Million Particles via angular--averaged Ewald potential: A Monte Carlo study

“…The AAEP was correctly presented for a TCP without a clear derivation [53]. It was successfully used in computations [54][55][56][57][58][59][60][61][62][63][64][65], including the simulation of quantum systems [11][12][13]. Recently we have succeeded to find a step by step derivation of the AAEP for a TCP [66].…”