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s_6/MD | MC3 lipid CpHMD parametrization test (dV/dl coefficients, before Boltzmann reweighting) | MDRepo
Records
MC3 lipid CpHMD parametrization test (dV/dl coefficients, before Boltzmann reweighting)
Experiments
s_6/MD
Overview
MD-A00C7T
MC3 lipid CpHMD parametrization test (dV/dl coefficients, before Boltzmann reweighting)
Back to record
Overview
Trajectory viewer
Analyses
Warnings
Cross-PBC contacts detected in 4/2001 frames. Non-PBC molecules appear to contact each other across periodic boundaries. Frame 192 has the most atoms in contact (12). Closest pairs in this frame: M1(MC3T).H94R (index 111) — S4675(BUF).BUF (index 126) (3.12 Å) M1(MC3T).H96R (index 117) — S4675(BUF).BUF (index 126) (3.34 Å) M1(MC3T).C94 (index 110) — S4675(BUF).BUF (index 126) (4.17 Å) M1(MC3T).C96 (index 116) — S4675(BUF).BUF (index 126) (4.30 Å) M1(MC3T).H96S (index 118) — S4675(BUF).BUF (index 126) (4.42 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
Counter-Ions
Cations (+)
0
Anions (-)
0
Total ions
0
0
residues