Free energy interactions

This section describes the \(\lambda\)-dependence of the potentials used for free energy calculations (see sec. Free energy calculations). All common types of potentials and constraints can be interpolated smoothly from state A (\(\lambda=0\)) to state B (\(\lambda=1\)) and vice versa. All bonded interactions are interpolated by linear interpolation of the interaction parameters. Non-bonded interactions can be interpolated linearly or via soft-core interactions.

Starting in GROMACS 4.6, \(\lambda\) is a vector, allowing different components of the free energy transformation to be carried out at different rates. Coulomb, Lennard-Jones, bonded, and restraint terms can all be controlled independently, as described in the mdp options.

Harmonic potentials

The example given here is for the bond potential, which is harmonic in GROMACS. However, these equations apply to the angle potential and the improper dihedral potential as well.

(1)\[\begin{split}\begin{aligned} V_b &=&{\frac{1}{2}}\left[{(1-{\lambda})}k_b^A + {\lambda}k_b^B\right] \left[b - {(1-{\lambda})}b_0^A - {\lambda}b_0^B\right]^2 \\ {\frac{\partial V_b}{\partial {\lambda}}}&=&{\frac{1}{2}}(k_b^B-k_b^A) \left[b - {(1-{\lambda})}b_0^A + {\lambda}b_0^B\right]^2 + \nonumber\\ & & \phantom{{\frac{1}{2}}}(b_0^A-b_0^B) \left[b - {(1-{\lambda})}b_0^A -{\lambda}b_0^B\right] \left[{(1-{\lambda})}k_b^A + {\lambda}k_b^B \right]\end{aligned}\end{split}\]

GROMOS-96 bonds and angles

Fourth-power bond stretching and cosine-based angle potentials are interpolated by linear interpolation of the force constant and the equilibrium position. Formulas are not given here.

Proper dihedrals

For the proper dihedrals, the equations are somewhat more complicated:

(2)\[\begin{split}\begin{aligned} V_d &=&\left[{(1-{\lambda})}k_d^A + {\lambda}k_d^B \right] \left( 1+ \cos\left[n_{\phi} \phi - {(1-{\lambda})}\phi_s^A - {\lambda}\phi_s^B \right]\right)\\ {\frac{\partial V_d}{\partial {\lambda}}}&=&(k_d^B-k_d^A) \left( 1+ \cos \left[ n_{\phi} \phi- {(1-{\lambda})}\phi_s^A - {\lambda}\phi_s^B \right] \right) + \nonumber\\ &&(\phi_s^B - \phi_s^A) \left[{(1-{\lambda})}k_d^A - {\lambda}k_d^B\right] \sin\left[ n_{\phi}\phi - {(1-{\lambda})}\phi_s^A - {\lambda}\phi_s^B \right]\end{aligned}\end{split}\]

Note: that the multiplicity \(n_{\phi}\) can not be parameterized because the function should remain periodic on the interval \([0,2\pi]\).

Tabulated bonded interactions

For tabulated bonded interactions only the force constant can interpolated:

(3)\[\begin{split}\begin{aligned} V &=& ({(1-{\lambda})}k^A + {\lambda}k^B) \, f \\ {\frac{\partial V}{\partial {\lambda}}} &=& (k^B - k^A) \, f\end{aligned}\end{split}\]

Coulomb interaction

The Coulomb interaction between two particles of which the charge varies with \({\lambda}\) is:

(4)\[\begin{split}\begin{aligned} V_c &=& \frac{f}{{\varepsilon_{rf}}{r_{ij}}}\left[{(1-{\lambda})}q_i^A q_j^A + {\lambda}\, q_i^B q_j^B\right] \\ {\frac{\partial V_c}{\partial {\lambda}}}&=& \frac{f}{{\varepsilon_{rf}}{r_{ij}}}\left[- q_i^A q_j^A + q_i^B q_j^B\right]\end{aligned}\end{split}\]

where \(f = \frac{1}{4\pi \varepsilon_0} = {138.935\,458}\) (see chapter Definitions and Units).

Coulomb interaction with reaction field

The Coulomb interaction including a reaction field, between two particles of which the charge varies with \({\lambda}\) is:

(5)\[\begin{split}\begin{aligned} V_c &=& f\left[\frac{1}{{r_{ij}}} + k_{rf}~ {r_{ij}}^2 -c_{rf}\right] \left[{(1-{\lambda})}q_i^A q_j^A + {\lambda}\, q_i^B q_j^B\right] \\ {\frac{\partial V_c}{\partial {\lambda}}}&=& f\left[\frac{1}{{r_{ij}}} + k_{rf}~ {r_{ij}}^2 -c_{rf}\right] \left[- q_i^A q_j^A + q_i^B q_j^B\right] \end{aligned}\end{split}\]

Note that the constants \(k_{rf}\) and \(c_{rf}\) are defined using the dielectric constant \({\varepsilon_{rf}}\) of the medium (see sec. Coulomb interaction with reaction field).

Lennard-Jones interaction

For the Lennard-Jones interaction between two particles of which the atom type varies with \({\lambda}\) we can write:

(6)\[\begin{split}\begin{aligned} V_{LJ} &=& \frac{{(1-{\lambda})}C_{12}^A + {\lambda}\, C_{12}^B}{{r_{ij}}^{12}} - \frac{{(1-{\lambda})}C_6^A + {\lambda}\, C_6^B}{{r_{ij}}^6} \\ {\frac{\partial V_{LJ}}{\partial {\lambda}}}&=&\frac{C_{12}^B - C_{12}^A}{{r_{ij}}^{12}} - \frac{C_6^B - C_6^A}{{r_{ij}}^6} \end{aligned}\end{split}\]

It should be noted that it is also possible to express a pathway from state A to state B using \(\sigma\) and \(\epsilon\) (see (5)). It may seem to make sense physically to vary the force field parameters \(\sigma\) and \(\epsilon\) rather than the derived parameters \(C_{12}\) and \(C_{6}\). However, the difference between the pathways in parameter space is not large, and the free energy itself does not depend on the pathway, so we use the simple formulation presented above.

Kinetic Energy

When the mass of a particle changes, there is also a contribution of the kinetic energy to the free energy (note that we can not write the momentum \(\mathbf{p}\) as m \(\mathbf{v}\), since that would result in the sign of \({\frac{\partial E_k}{\partial {\lambda}}}\) being incorrect 99):

(7)\[\begin{split}\begin{aligned} E_k &=& {\frac{1}{2}}\frac{\mathbf{p}^2}{{(1-{\lambda})}m^A + {\lambda}m^B} \\ {\frac{\partial E_k}{\partial {\lambda}}}&=& -{\frac{1}{2}}\frac{\mathbf{p}^2(m^B-m^A)}{({(1-{\lambda})}m^A + {\lambda}m^B)^2}\end{aligned}\end{split}\]

after taking the derivative, we can insert \(\mathbf{p}\) = m \(\mathbf{v}\), such that:

(8)\[{\frac{\partial E_k}{\partial {\lambda}}}~=~ -{\frac{1}{2}}\mathbf{v}^2(m^B-m^A)\]

Constraints

The constraints are formally part of the Hamiltonian, and therefore they give a contribution to the free energy. In GROMACS this can be calculated using the LINCS or the SHAKE algorithm. If we have \(k = 1 \ldots K\) constraint equations \(g_k\) for LINCS, then

(9)\[g_k = | \mathbf{r}_{k} | - d_{k}\]

where \(\mathbf{r}_k\) is the displacement vector between two particles and \(d_k\) is the constraint distance between the two particles. We can express the fact that the constraint distance has a \({\lambda}\) dependency by

(10)\[d_k = {(1-{\lambda})}d_{k}^A + {\lambda}d_k^B\]

Thus the \({\lambda}\)-dependent constraint equation is

(11)\[g_k = | \mathbf{r}_{k} | - \left({(1-{\lambda})}d_{k}^A + {\lambda}d_k^B\right).\]

The (zero) contribution \(G\) to the Hamiltonian from the constraints (using Lagrange multipliers \(\lambda_k\), which are logically distinct from the free-energy \({\lambda}\)) is

(12)\[\begin{split}\begin{aligned} G &=& \sum^K_k \lambda_k g_k \\ {\frac{\partial G}{\partial {\lambda}}} &=& \frac{\partial G}{\partial d_k} {\frac{\partial d_k}{\partial {\lambda}}} \\ &=& - \sum^K_k \lambda_k \left(d_k^B-d_k^A\right)\end{aligned}\end{split}\]

For SHAKE, the constraint equations are

(13)\[g_k = \mathbf{r}_{k}^2 - d_{k}^2\]

with \(d_k\) as before, so

(14)\[\begin{aligned} {\frac{\partial G}{\partial {\lambda}}} &=& -2 \sum^K_k \lambda_k \left(d_k^B-d_k^A\right)\end{aligned}\]

Soft-core interactions

Fig. 32 Soft-core interactions at \({\lambda}=0.5\), with \(p=2\) and \(C_6^A=C_{12}^A=C_6^B=C_{12}^B=1\).

In a free-energy calculation where particles grow out of nothing, or particles disappear, using the the simple linear interpolation of the Lennard-Jones and Coulomb potentials as described in (6) and (5) may lead to poor convergence. When the particles have nearly disappeared, or are close to appearing (at \({\lambda}\) close to 0 or 1), the interaction energy will be weak enough for particles to get very close to each other, leading to large fluctuations in the measured values of \(\partial V/\partial {\lambda}\) (which, because of the simple linear interpolation, depends on the potentials at both the endpoints of \({\lambda}\)).

To circumvent these problems, the singularities in the potentials need to be removed. This can be done by modifying the regular Lennard-Jones and Coulomb potentials with “soft-core” potentials that limit the energies and forces involved at \({\lambda}\) values between 0 and 1, but not at \({\lambda}=0\) or 1.

In GROMACS the soft-core potentials \(V_{sc}\) are shifted versions of the regular potentials, so that the singularity in the potential and its derivatives at \(r=0\) is never reached:

(15)\[\begin{split}\begin{aligned} V_{sc}(r) &=& {(1-{\lambda})}V^A(r_A) + {\lambda}V^B(r_B) \\ r_A &=& \left(\alpha \sigma_A^6 {\lambda}^p + r^6 \right)^\frac{1}{6} \\ r_B &=& \left(\alpha \sigma_B^6 {(1-{\lambda})}^p + r^6 \right)^\frac{1}{6}\end{aligned}\end{split}\]

where \(V^A\) and \(V^B\) are the normal “hard core” Van der Waals or electrostatic potentials in state A (\({\lambda}=0\)) and state B (\({\lambda}=1\)) respectively, \(\alpha\) is the soft-core parameter (set with sc_alpha in the mdp file), \(p\) is the soft-core \({\lambda}\) power (set with sc_power), \(\sigma\) is the radius of the interaction, which is \((C_{12}/C_6)^{1/6}\) or an input parameter (sc_sigma) when \(C_6\) or \(C_{12}\) is zero.

For intermediate \({\lambda}\), \(r_A\) and \(r_B\) alter the interactions very little for \(r > \alpha^{1/6} \sigma\) and quickly switch the soft-core interaction to an almost constant value for smaller \(r\) (Fig. 32). The force is:

(16)\[F_{sc}(r) = -\frac{\partial V_{sc}(r)}{\partial r} = {(1-{\lambda})}F^A(r_A) \left(\frac{r}{r_A}\right)^5 + {\lambda}F^B(r_B) \left(\frac{r}{r_B}\right)^5\]

where \(F^A\) and \(F^B\) are the “hard core” forces. The contribution to the derivative of the free energy is:

(17)\[\begin{split}\begin{aligned} {\frac{\partial V_{sc}(r)}{\partial {\lambda}}} & = & V^B(r_B) -V^A(r_A) + {(1-{\lambda})}\frac{\partial V^A(r_A)}{\partial r_A} \frac{\partial r_A}{\partial {\lambda}} + {\lambda}\frac{\partial V^B(r_B)}{\partial r_B} \frac{\partial r_B}{\partial {\lambda}} \nonumber\\ &=& V^B(r_B) -V^A(r_A) + \nonumber \\ & & \frac{p \alpha}{6} \left[ {\lambda}F^B(r_B) r^{-5}_B \sigma_B^6 {(1-{\lambda})}^{p-1} - {(1-{\lambda})}F^A(r_A) r^{-5}_A \sigma_A^6 {\lambda}^{p-1} \right]\end{aligned}\end{split}\]

The original GROMOS Lennard-Jones soft-core function100 uses \(p=2\), but \(p=1\) gives a smoother \(\partial H/\partial{\lambda}\) curve. Another issue that should be considered is the soft-core effect of hydrogens without Lennard-Jones interaction. Their soft-core \(\sigma\) is set with sc_sigma in the mdp file. These hydrogens produce peaks in \(\partial H/\partial{\lambda}\) at \({\lambda}\) is 0 and/or 1 for \(p=1\) and close to 0 and/or 1 with \(p=2\). Lowering sc_sigma will decrease this effect, but it will also increase the interactions with hydrogens relative to the other interactions in the soft-core state.

When soft-core potentials are selected (by setting sc_alpha >0), and the Coulomb and Lennard-Jones potentials are turned on or off sequentially, then the Coulombic interaction is turned off linearly, rather than using soft-core interactions, which should be less statistically noisy in most cases. This behavior can be overwritten by using the mdp option sc-coul to yes. Note that the sc-coul is only taken into account when lambda states are used, not with couple-lambda0  / couple-lambda1, and you can still turn off soft-core interactions by setting sc-alpha=0. Additionally, the soft-core interaction potential is only applied when either the A or B state has zero interaction potential. If both A and B states have nonzero interaction potential, default linear scaling described above is used. When both Coulombic and Lennard-Jones interactions are turned off simultaneously, a soft-core potential is used, and a hydrogen is being introduced or deleted, the sigma is set to sc-sigma-min, which itself defaults to sc-sigma-default.

Recently, a new formulation of the soft-core approach has been derived that in most cases gives lower and more even statistical variance than the standard soft-core path described above 101, 102. Specifically, we have:

(18)\[\begin{split}\begin{aligned} V_{sc}(r) &=& {(1-{\lambda})}V^A(r_A) + {\lambda}V^B(r_B) \\ r_A &=& \left(\alpha \sigma_A^{48} {\lambda}^p + r^{48} \right)^\frac{1}{48} \\ r_B &=& \left(\alpha \sigma_B^{48} {(1-{\lambda})}^p + r^{48} \right)^\frac{1}{48}\end{aligned}\end{split}\]

This “1-1-48” path is also implemented in GROMACS. Note that for this path the soft core \(\alpha\) should satisfy \(0.001 < \alpha < 0.003\), rather than \(\alpha \approx 0.5\).