26 lines
987 B
Python
26 lines
987 B
Python
import mdevaluate as md
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import numpy as np
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path_to_sim = "/data/skloth/sim/IL_water/C4MIM_BF4_x50/T300_nvt"
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trajectory = md.open(path_to_sim, topology="run.tpr", trajectory="out/traj_full.xtc")
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print(trajectory[0].atom_names)
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print(trajectory[0].residue_names)
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print(np.unique(trajectory[0].atom_names))
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print(np.unique(trajectory[0].residue_names))
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print(np.unique(trajectory[0].atom_names[trajectory[0].residue_names == "amim"]))
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print(np.unique(trajectory[0].atom_names[trajectory[0].residue_names == "BF4"]))
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print(np.unique(trajectory[0].atom_names[trajectory[0].residue_names == "SOL"]))
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carbon_atoms = trajectory.subset(atom_name="C")
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hydrogen_atoms = trajectory.subset(atom_name="H")
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cation_chain_end_atoms = trajectory.subset(atom_name="CT")
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cation_atoms = trajectory.subset(residue_name="amim")
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anion_atoms = trajectory.subset(residue_name="BF4")
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water_atoms = trajectory.subset(residue_name="SOL")
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hydrogen_water = trajectory.subset(atom_name="HW", residue_name="SOL")
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