Table 1.
Implementation and availability of multi-scale methods from figure 1.
| panel | model | MD engine |
|---|---|---|
| a, e | PACE/MARTINI (https://www.ks.uiuc.edu/~whan/PACE) [25,73] | modified version of NAMD 2.9 GROMACS (http://www.gromacs.org) [117] |
| a, e | ELBA [26], FG/ELBA [72] (http://www.orsi.sems.qmul.ac.uk/elba) | LAMMPS (https://lammps.sandia.gov) [118] |
| b | FG/GROMOS CG [31] | GROMOS11 (http://www.gromos.net) [119] |
| b, f, i | SIRAH (www.sirahff.com) | AMBER (http://ambermd.org) [120] GROMACS (http://www.gromacs.org) [117] |
| c | AdResS [46] | ESPResSo++ (http://www.espresso-pp.de) [121] GROMACS (http://www.gromacs.org) [117] |
| c | PE-AdResS [37] | modified version of GROMACS |
| c | GC-AdResS [38,39] | modified version of GROMACS 5.1.0 |
| c, g | H-AdResS [34,35] | ESPResSo++ (http://www.espresso-pp.de) [121] LAMMPS (https://lammps.sandia.gov) [118] |
| c | RelRes [51] | GROMACS (http://www.gromacs.org) [117] |
| d, h | MARTINI virtual sites [52], GROMOS/MARTINI [53] (http://cgmartini.nl) | GROMACS (http://www.gromacs.org) [117] |
| f | GROMOS/Gō [76] | modified version of GROMACS 4.5 |
| i | OPLS/Gō [61], AMBER/Gō [62] | library-based Monte Carlo (LBMC) (https://www.csb.pitt.edu/Faculty/zuckerman/software.html) [122] |
| i | CHARMM/ERM [63] | NAMD2 (http://www.ks.uiuc.edu/Research/namd) [123] and in-house code |
| i | CHARMM/PRIMO [65] | CHARMM c38a2 or later (https://www.charmm.org) [124] |
| j | AA + CG (CHARMM/MARTINI) [66] | in-house version of QM4D (http://www.qm4d.info) |
| k | GROMOS/ATTRACT [68] | in-house code |
| k | polymer solutions [69,70] | modified version of IBIsCO (http://www.theo.chemie.tu-darmstadt.de/ibisco) [125] |