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MC3 lipid CpHMD parametrization test (dV/dl coefficients, after Boltzmann reweighting)
Experiments
s_7/MD
Overview
MD-A00C7U
MC3 lipid CpHMD parametrization test (dV/dl coefficients, after Boltzmann reweighting)
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Overview
Trajectory viewer
Analyses
Warnings
Cross-PBC contacts detected in 2/2001 frames. Non-PBC molecules appear to contact each other across periodic boundaries. Frame 401 has the most atoms in contact (7). Closest pairs in this frame: M1(MC3T).H15S (index 38) — S4675(BUF).BUF (index 126) (3.96 Å) M1(MC3T).H13R (index 31) — S4675(BUF).BUF (index 126) (4.11 Å) M1(MC3T).H16S (index 41) — S4675(BUF).BUF (index 126) (4.39 Å) M1(MC3T).C15 (index 36) — S4675(BUF).BUF (index 126) (4.88 Å) M1(MC3T).H16R (index 40) — S4675(BUF).BUF (index 126) (4.89 Å) etc. (6 pairs)
Force Field & Water Model
Force field
CHARMM36
Water model
TIP3P
Simulation Parameters
Frames
2,001
Frequency
50 ps
Simulation length
100.05 ns
Timestep
2 fs
Temperature
300 K
Ensemble
NPT
Simulation Box
Box type
cubic
X
52.222 nm
Y
52.222 nm
Z
52.222 nm
Box volume
142,416.13 nm³
System Composition
Total system
129
atoms
4
residues
Protein
0
atoms
0
residues
Nucleic acids
0
atoms
0
residues
Lipids
0
atoms
0
residues
Carbohydrates
0
atoms
0
residues
Solvent
0
atoms
0
residues
Counter-Ions
Cations (+)
0
Anions (-)
0
Total ions
0