I'm about to start protein-peptide simulations to estimate binding affinity via umbrella sampling. Is it OK to perform it using implicit salvation? Could not find works with this approach using GRAMACS.
It depends on your systems of interest, the property you are aiming to calculate, and the accuracy you are satisfied with. Umbrella sampling is not generally recommended using implicit solvent, but in principal, it can give you some basic estimates. This can especially be helpful if you comparing binding affinity of different ligands! However, you want be careful to use implicit solvent when you know the ligands or the accepting packet are hydrophilic! Generally speaking, water molecules can play important roles via forming hydrogen bonds with the lignads or the packet! Do not hesitate to contact me if you have any further questions!
It depends on your systems of interest, the property you are aiming to calculate, and the accuracy you are satisfied with. Umbrella sampling is not generally recommended using implicit solvent, but in principal, it can give you some basic estimates. This can especially be helpful if you comparing binding affinity of different ligands! However, you want be careful to use implicit solvent when you know the ligands or the accepting packet are hydrophilic! Generally speaking, water molecules can play important roles via forming hydrogen bonds with the lignads or the packet! Do not hesitate to contact me if you have any further questions!
I used implicit solvent in REMD protein self-assembly investigations. First, performed using explicit water model and repeted simulation in the same system but using implicit solvent. Free energy landscape gave almost the same result, then I reached longer time scale simulation using implicit solvent model. You can check my Soft matter paper: Prediction of the structure of a silk-like protein in oligomeric states using explicit and implicit solvent models.
Moreover, using implicit solvent in umbrella simulation maybe gives improper results but running simulation using bosh implicit as well as explict solvent you can compare results and decide what to do.