diff --git a/src/multiego/topology.py b/src/multiego/topology.py index 54fa04f3..439c4850 100644 --- a/src/multiego/topology.py +++ b/src/multiego/topology.py @@ -349,7 +349,9 @@ def get_lj_pairs(topology): lj_pairs = pd.DataFrame(columns=["ai", "aj", "epsilon", "sigma"], index=np.arange(len(topology.parameterset.nbfix_types))) for i, (sbtype_i, sbtype_j) in enumerate(topology.parameterset.nbfix_types): key = (sbtype_i, sbtype_j) - c12, c6 = topology.parameterset.nbfix_types[key][0] * 4.184, topology.parameterset.nbfix_types[key][1] * 0.1 + # This is read as rmin not as sigma --> must be scaled by 1/2**(1/6) + # Any contact present more then once is overwritten by the last one in the nonbond_params + c12, c6 = topology.parameterset.nbfix_types[key][0] * 4.184, topology.parameterset.nbfix_types[key][1] * 0.1 / (2**(1/6)) epsilon = c6**2 / (4 * c12) if c6 > 0 else -c12 sigma = (c12 / c6) ** (1 / 6) if c6 > 0 else c12 ** (1 / 12) / (2.0 ** (1.0 / 6.0)) lj_pairs.loc[i] = [sbtype_i, sbtype_j, epsilon, sigma]