References.md

test/ff3/amber03

Duan et al. (2003), J. Comp. Chem. 24, 1999-2012
Parameter sets obtained from AmberTools v17

test/ff3/amber99

Wang et al. (2000), J. Comp. Chem. 21, 1049-1074
Parameter sets obtained from AmberTools v17

test/ff3/charmm27

MacKerell et al. (2004), J. Comp. Chem. 25, 1400-1415 (protein cmap)
MacKerell et al. (1998), J. Phys. Chem. B. 102, 3586-3616 (proteins)
Foloppe et al. (2000), J. Comp. Chem. 21, 86-104 (nucleic acids)
MacKerell et al. (2000), J. Comp. Chem. 21, 105-120 (nucleic acids)
Feller et al. (2000), J. Phys. Chem. B. 104, 7510-7515 (lipids)
Feller et al. (2002), J. Am. Chem. Soc. 124, 318-326 (lipids)
Beglov et al. (1994), J. Chem. Phys. 100, 9050-9063 (ions)
URL: http://mackerell.umaryland.edu/CHARMM_ff_params_files/toppar_c35b2_c36a2.tgz

test/ff3/charmm36_ions_nbfix

Won et al. (2012) J. Phys. Chem A. 116, 11763-11767
Beglov et al. (1994) J. Chem. Phys 100, 9050-9063
URL: http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

test/ff3/charmm36_lipids

Lim et al. (2012), J. Phys. Chem. B, 116 203-210
Klauda et al. (2012), J. Phys. Chem. B, 116  9424-9431
Klauda et al. (2010), J. Phys. Chem. B, 114, 7830-7843
URL: from http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

test/ff3/tip3p

Jorgensen et al. (1983) Mol. Phys. 79, 926
Parameters as tabulated in: Mahoney et al (2000) J. Chem. Phys. 112, 8910

test/ff3/tip4p

Jorgensen et al. (1985) Mol. Phys. 56, 1381
Parameters as tabulated in: Mahoney et al. (2000) J. Chem. Phys. 112, 8910