[gmx-users] bad contacts and/or reduc

Dear gmx-users We want to study interaction of ligand to enzyme. We constructed the gro and top file from Prodrg and add it to the end of enzyme gro and change the number of atoms. Some of calculation carried out until mdrun of pr.mdp, but in this step we encontered to following error. what is the

Re: [gmx-users] bad contacts and/or reduc

Hi Davood,Although there could be many causes, in this case I'd suspect that there is a water molecule trapped inside the protein. This can be the result of solvation using genbox. An isolated water molecule can start to rattle. It will get close to one side of the microcavity and kicked to the