Enter a unique name to identify your simulation. For example, 'protein_simulation1'. No specific rules apply.
Upload the protein structure file you want to simulate. Supported formats are .pdb and .gro. You can prepare your own file or download one from the PDB database.
Drag & Drop or Click to Browse (Supported: .pdb, .gro)
Specify the duration for NPT equilibration before starting the simulation. 100 ps is typically sufficient to stabilize the system.
Specify the duration for NPT equilibration before starting the simulation. 100 ps is typically sufficient to stabilize the system.
020
Specify the duration for NVT equilibration before simulation. Setting it around 100 ps is recommended to achieve system stability.
020
Set the total duration for the main MD simulation. For beginners, around 15 ns (15000 ps) is a good starting point.
020
Set the NaCl salt concentration to mimic physiological conditions. 0.15 M (mol/L) is recommended to match human body environments.
00.1
Specify the simulation temperature in Kelvin (K). A typical value for biological systems is around 300 K.
0600
Specify the distance threshold (in nm) used for clustering analysis based on trajectory data.
00.1
Specify the algorithm or method name for trajectory clustering (e.g., linkage method).
Choose the shape of the simulation box that surrounds the protein. 'Dodecahedron' is recommended for efficiency and stability.
Select the water model to fill the simulation box. TIP3P is a widely used and reliable choice for general protein simulations.
Select how to handle periodic boundary conditions (PBC) during analysis. 'noPBC' makes it easier to observe protein movements clearly.
