From cf81ec1714d2ca610f790c1937fe3ecb188218f9 Mon Sep 17 00:00:00 2001 From: Bruno Stegani Date: Tue, 26 Nov 2024 14:44:01 +0100 Subject: [PATCH] fixed sigma definition --- src/multiego/topology.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/multiego/topology.py b/src/multiego/topology.py index 9f5da623..e3211eef 100644 --- a/src/multiego/topology.py +++ b/src/multiego/topology.py @@ -349,8 +349,8 @@ 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] * 4.184 - epsilon = c6**2 / (4 * c12) if c6 > 0 else 0 + c12, c6 = topology.parameterset.nbfix_types[key][0] * 4.184, topology.parameterset.nbfix_types[key][1] * 0.1 + epsilon = c6**2 / (4 * c12) if c6 > 0 else 0 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] @@ -377,7 +377,7 @@ def get_lj14_pairs(topology): { "ai": pair.atom1.type, "aj": pair.atom2.type, - "c6": pair.type.rmin * 4.184, + "c6": pair.type.sigma * 0.1, "c12": pair.type.epsilon * 4.184, } for pair in top[0].adjusts