Hi Dear researchers
I am trying to understand the mechanism action and the correct orientation of a small molecule to an Ag Nanoparticle. I want accomplish that by simulating them with Gromacs package (molecular dynamics simulation), when i was simulating the system, i found out that the ligands aggregare and don't interact with the nanoparticle but the experimental results show that the ligand does interact with the nanoparticle. I think if i run the simulation for longer time this problem might be solved but i don't have enough computing resource.
How should I solve this problem without running the MD for a long time?
What should I do to the ligands not to aggregate.
a movie of the simulation with one ligands is attached.
Interaction of ligands with Ag nanoparticle depends on their interaction parameters (check your parameters). For aggregation, what was your initial configuration file? I mean, did you tried ligands on different faces in your initial configuration file?
Hi Bagheri
As suggested by shrivastav, Its depend on parameter as well as initial configuration. One thing you can do that during the MD simulation, you can apply position restraint on your ligand and might be your problem will be solved.
Regards,
Nandan
Check your sigma and epsilon parameters and also,you could try bringing down the concentration of your system. In that way, you don't have to use more computational resources. Just give it a try.
Hi
First check would be force field parameter. Let's assume if that is correct then you may constrained the nanoparticle in the middle of the simulation box and let ligand fly around it. This may save your computation time significantly.
The concentration of ligand plays important role here since it is competition between ligand-ligand and Ag-ligand interaction. Check the concentration used in the experiment and set up your simulation accordingly.
Your system may be stuck at a local minima of potential energy surface. The experimental thing may come after ~100 ns or even ~microsecond (unpredictable!!)
Here is a quick solution,
Start with the ligand bound to Ag_NP state (that is, the initial state) and run it using gromos53a6ff. If you see they are stable for a few ns (~40-50 ns), you can say they are stable that way. If possible, run a metadynamics simulation.
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