Methotrexate (MTX) 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 | 53 |
| Molecule charge (simulated) | -2 |
| System number of atoms | 1979 |
| 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 | 0.72 | 0.73 | 0.74 | 0.74 | 0.75 | 0.75 | 0.75 | 0.76 | 0.76 | 0.77 | 0.77 | 0.78 | 0.78 | 0.79 | 0.79 |
| # Exchanges | 3638 | 3638 | 3745 | 3676 | 3728 | 3763 | 3788 | 3800 | 3799 | 3807 | 3799 | 3883 | 3860 | 3957 | 3951 |
| Avg. # Exchanges | 0.73 | 0.73 | 0.75 | 0.74 | 0.75 | 0.75 | 0.76 | 0.76 | 0.76 | 0.76 | 0.76 | 0.78 | 0.77 | 0.79 | 0.79 |
RMSd Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| RMSd_first | 2.5538 | 0.6516 |
| RMSd_exp | 2.4138 | 0.5087 |
| RMSdist_first | 1.5420 | 0.6528 |
| RMSdist_exp | 1.2992 | 0.3510 |
RMSd Plot
Rgyr Averages
Reduced chart version
| Name | Average (Å) | Standard deviation (Å) |
|---|---|---|
| Rgyr | 5.4123 | 0.4402 |
| RgyrX | 2.7207 | 0.1570 |
| RgyrY | 4.9879 | 0.4681 |
| RgyrZ | 5.1128 | 0.5537 |
Rgyr Plot
Fluctuation Averages
| Name | Atomic_Fluct |
| Average (Å) | 1.7805 |
| Standard deviation (Å) | 0.6474 |
Atoms list
| Atom name | Fluctuation (Å) |
|---|---|
| N1 | 1.918 |
| C2 | 1.834 |
| NA2 | 2.578 |
| N3 | 1.89 |
| C4 | 1.674 |
| NA4 | 2.793 |
| C4A | 0.856 |
| N5 | 1.233 |
| C6 | 1.078 |
| C7 | 1.59 |
| N8 | 1.896 |
| C8A | 1.209 |
| C9 | 1.856 |
| N10 | 1.793 |
| CM | 2.729 |
| C11 | 0.769 |
| C12 | 1.406 |
| C13 | 1.568 |
| C14 | 1.307 |
| C15 | 1.659 |
| C16 | 1.465 |
| C | 1.054 |
| O | 2.006 |
| N | 0.86 |
| CA | 1.204 |
| CT | 2.26 |
| O1 | 2.934 |
| O2 | 2.946 |
| CB | 1.035 |
| CG | 1.505 |
| CD | 2.217 |
| OE1 | 2.827 |
| OE2 | 2.806 |
3D View
Fluctuation Plot