AlkaneStudy.Gromacs

This Github repository accompanies the article

Benchmarking of Molecular Dynamics Force Fields for Solid–Liquid and Solid–Solid Phase Transitions in Alkanes

Stephen A. Burrows, Ivan Korotkin, Stoyan K. Smoukov, Edo S. Boek, and Sergey Karabasov

J. Phys. Chem. B 2021, 125, 19, 5145–5159

doi.org/10.1021/acs.jpcb.0c07587

Force field .mdp settings

PYS-W

Paul, W., Yoon, D. Y. and Smith, G. D. (1995) ‘An optimized united atom model for simulations of polymethylene melts’, The Journal of Chemical Physics, 103(4), pp. 1702–1709. doi: 10.1063/1.469740.

dt                      = 0.002
cutoff-scheme           = Verlet
coulombtype             = Cut-off ; no charges
rcoulomb                = 1.0
vdwtype                 = Cut-off
rvdw                    = 1.0
DispCorr                = EnerPres

TraPPE-UA

Martin, M. G. and Siepmann, J. I. (1998) ‘Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes’, Journal of Physical Chemistry B, 102(14), pp. 2569–2577. doi: 10.1021/jp972543+.

dt                      = 0.002
cutoff-scheme           = Verlet
coulombtype             = PME ; Cut-off if no charges present
rcoulomb                = 1.4
vdwtype                 = Cut-off
rvdw                    = 1.4
DispCorr                = EnerPres
constraints             = all-bonds

L-OPLS

Siu, S. W. I., Pluhackova, K. and Böckmann, R. A. (2012) ‘Optimization of the OPLS-AA force field for long hydrocarbons’, Journal of Chemical Theory and Computation, 8(4), pp. 1459–1470. doi: 10.1021/ct200908r.

dt                      = 0.002
cutoff-scheme           = Verlet
coulombtype             = PME
rcoulomb                = 1.3
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw-switch             = 1.1
rvdw                    = 1.3
DispCorr                = EnerPres
constraints             = h-bonds

CHARMM

Klauda, J. B. et al. (2010) ‘Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types’, Journal of Physical Chemistry B, 114(23), pp. 7830–7843. doi: 10.1021/jp101759q.

dt                      = 0.001
cutoff-scheme           = Verlet
coulombtype             = PME
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw-switch             = 1.0
rvdw                    = 1.2
constraints             = h-bonds

COMPASS-gmx

Sun, H. (1998) ‘Compass: An ab initio force-field optimized for condensed-phase applications - Overview with details on alkane and benzene compounds’, Journal of Physical Chemistry B, pp. 7338–7364. doi: 10.1021/jp980939v.

The 9-6 Lennard-Jones potential must be tabulated, hence vdwtype = User.

dt                      = 0.001
cutoff-scheme           = group
rlist                   = 1.1
coulombtype             = PME
rcoulomb                = 1.0
vdwtype                 = User
vdw-modifier            = Potential-shift
rvdw                    = 1.0
DispCorr                = EnerPres
constraints             = h-bonds

Williams 7B

Pair potential: Williams, D. E. (1967) ‘Nonbonded potential parameters derived from crystalline hydrocarbons’, The Journal of Chemical Physics, 47(11), pp. 4680–4684. doi: 10.1063/1.1701684.

Torsion potential: Tu, K., Tobias, D. J. and Klein, M. L. (1995), Journal of Physical Chemistry, 99(24), pp. 10035–10042. doi: 10.1021/j100024a053.

dt                      = 0.001
cutoff-scheme           = group ; if using tabulated potential
rlist                   = 1.05
coulombtype             = Cut-off ; no charges
rcoulomb                = 1.0
vdwtype                 = Cut-off
vdw-modifier            = Potential-shift
rvdw                    = 1.0
DispCorr                = EnerPres
constraints             = h-bonds