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MC3 lipid CpHMD parametrization test (dV/dl coefficients, before Boltzmann reweighting)
Experiments
s_8/MD
Overview
MD-A00C7T
MC3 lipid CpHMD parametrization test (dV/dl coefficients, before Boltzmann reweighting)
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Overview
Trajectory viewer
Analyses
Warnings
Cross-PBC contacts detected in 5/2001 frames. Non-PBC molecules appear to contact each other across periodic boundaries. Frame 646 has the most atoms in contact (12). Closest pairs in this frame: M1(MC3T).H22S (index 80) — S4677(BUF).BUF (index 128) (2.80 Å) M1(MC3T).H21R (index 76) — S4677(BUF).BUF (index 128) (3.00 Å) M1(MC3T).H22R (index 79) — S4677(BUF).BUF (index 128) (3.26 Å) M1(MC3T).C22 (index 78) — S4677(BUF).BUF (index 128) (3.45 Å) M1(MC3T).H12S (index 29) — S4677(BUF).BUF (index 128) (3.51 Å) etc. (11 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
52.097 nm
Y
52.097 nm
Z
52.097 nm
Box volume
141,397.89 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