N-alpha-(2-naphthylsulfonyl)-n(3-amidino-l-phenylalaninyl)isopipecolinic acid methyl ester (FD2) Summary
TRAJECTORIES
METADATA
| Parameter | Value |
|---|---|
| Method | HamiltonianREMD |
| Number of MD replicas | 16 |
| Length of the MD simulations (ns) | 10 |
| Number of steps between exchanges | 100 |
| Force Field | General Amber Force Field (GAFF) |
| Charge scheme | Semi-Empirical (AM1) |
| REMD Progression | Geometric Progression |
| Initial (low) temperature (K) / Scaling factor | 298 / 1 |
| Final (high) temperature (K) / Scaling factor | 498 / 0.59 |
| Molecule number of atoms | 68 |
| Molecule charge (simulated) | 1 |
| System number of atoms | 2165 |
| Box size in simulations (nm) | 0.8 |
| Solvent model | TIP3P |
| Box type in simulations | Octahedron |
| MD ensemble | NVT |
REMD stats
| 1-2 | 2-3 | 3-4 | 4-5 | 5-6 | 6-7 | 7-8 | 8-9 | 9-10 | 10-11 | 11-12 | 12-13 | 13-14 | 14-15 | 15-16 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Probabilities | 0.78 | 0.78 | 0.79 | 0.79 | 0.79 | 0.81 | 0.80 | 0.81 | 0.81 | 0.82 | 0.82 | 0.82 | 0.83 | 0.83 | 0.83 |
| # Exchanges | 3900 | 3901 | 3926 | 3969 | 3986 | 4026 | 4047 | 4056 | 4027 | 4097 | 4128 | 4097 | 4167 | 4133 | 4153 |
| Avg. # Exchanges | 0.78 | 0.78 | 0.79 | 0.79 | 0.80 | 0.81 | 0.81 | 0.81 | 0.81 | 0.82 | 0.83 | 0.82 | 0.83 | 0.83 | 0.83 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.8981 | 0.7614 |
| RMSd_exp | 3.2020 | 0.9011 |
| RMSdist_first | 1.7318 | 0.5851 |
| RMSdist_exp | 1.7856 | 0.6590 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 4.5369 | 0.3205 |
| RgyrX | 3.4254 | 0.3161 |
| RgyrY | 3.8442 | 0.4961 |
| RgyrZ | 3.7895 | 0.3923 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 2.2534 |
| Standard deviation (Å) | 0.9228 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| C | 0.983 |
| C1 | 0.933 |
| C2 | 2.044 |
| C3 | 2.475 |
| C4 | 2.13 |
| C5 | 1.584 |
| C6 | 2.612 |
| N | 3.386 |
| N1 | 3.318 |
| C7 | 1.551 |
| C8 | 1.306 |
| C9 | 1.415 |
| O | 1.598 |
| N2 | 1.537 |
| C10 | 1.6 |
| C11 | 1.746 |
| C12 | 2.035 |
| C13 | 1.83 |
| C14 | 1.967 |
| C15 | 2.17 |
| O1 | 2.37 |
| O2 | 2.533 |
| C16 | 2.897 |
| N3 | 1.442 |
| S | 1.647 |
| O3 | 2.529 |
| O4 | 2.623 |
| C17 | 0.92 |
| C18 | 1.817 |
| C19 | 2.606 |
| C20 | 2.462 |
| C21 | 2.809 |
| C22 | 1.594 |
| C23 | 3.998 |
| C24 | 4.718 |
| C25 | 4.588 |
| C26 | 3.603 |
3D View
Fluctuation Plot