MDRepo
Browse
Communities
My depositions
New Deposition
EN
Log in
Records
MC3 lipid CpHMD parametrization test (dV/dl coefficients, after Boltzmann reweighting)
Experiments
s_1/MD
Overview
MD-A00C7U
MC3 lipid CpHMD parametrization test (dV/dl coefficients, after Boltzmann reweighting)
Back to record
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 73 has the most atoms in contact (5). Closest pairs in this frame: M1(MC3T).H97S (index 121) — S4675(BUF).BUF (index 126) (3.83 Å) M1(MC3T).H97R (index 120) — S4675(BUF).BUF (index 126) (4.19 Å) M1(MC3T).H98S (index 124) — S4675(BUF).BUF (index 126) (4.49 Å) M1(MC3T).C97 (index 119) — S4675(BUF).BUF (index 126) (4.54 Å)
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