I am working on a kinase-inhibitor complex. I wanted to perform a molecular dynamics simulation for the same. While going through the literature, I came across several options for the water model and force field to be used.
The literature reveals that SPC, TIP3P, and TIP4PEw are commonly used water models with different kinases. These have been used with force fields such as OPLS2005, CHARRM, and AMBER. Most report simulations with Desmond software. Some report NAMD and GROMACS.
Some studies report the Generalized Born Solvent models with coarse-grained force fields.
In such a situation, if I need to save some computation time then I need to use a three-point model (TIP3P or SPC).
How do I decide which one is better for studying kinase-inhibitor interactions and stability?
I have also read some question answers from Quora which mention TIP3P works better with OPLS. But I am still confused with this selection.
Further, I am also confused about the length of the simulation. Some papers have performed only 5ns for these protein-ligand interaction studies while some even go till 50ns.
As per my understanding from the literature, a simulation run that can indicate the stability of the complex and gives the desired information should be enough.
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