GROMACS version: 2021.5
GROMACS modification: Yes
Hi, dear GROMACS users. I try to perform a brownian dynamics simulation of a protein in water. I am a bit familiar with MD simulations of proteins in NAMD2 and i have recently begun learning GROMACS. I have started from the tutorial called “Lysozyme in water”, which is a regular MD simulation. However, i need to perform namely a brownian dynamics simulation of a protein. I know that for this purpose i should set the integrator to “bd”, but i get the error which tells that some water molecules cannot be settled at the production stage. The previous stages regarding to energy minimization and equilibration are made according to the “Lysozyme in water”. Could somebody tell me what exactly to do in order to perform a brownian dynamics simulation? Is there any tutorials dedicated to such kind of simlations? Could somebody share some examples of simulation files?