[gmx-users] Hydroxyl bonds rotating too much

Thank you Justin. The problematic OH is part of the cofactor molecule. This OH group is located in an extreme part of the cofactor so it apparently only interacts with solvent, not with the protein. I'm doing just now some tests of the cofactor solvated in order to check if the problem comes from

Re: [gmx-users] Hydroxyl bonds rotating too much

On 5/16/17 7:03 AM, Juan José Galano Frutos wrote: Hi there: I am simulating a protein which include as a cofactor a molecule bearing some hydroxyl groups. The system is crashing from the begining of the equilibration step (after the following steps: vaccuum minimization, solvating, neutralizi

[gmx-users] Hydroxyl bonds rotating too much

For more details, my system also has another cofactor with similar characteristics (FAD), I mean with hydroxyl groups but all is going fine with it so far (equilibration step). As I wrote before I did the following steps: 1- vaccuum minimization 2- solvating 3- neutralizing 4- minimization 5- heat

[gmx-users] Hydroxyl bonds rotating too much

Hi there: I am simulating a protein which include as a cofactor a molecule bearing some hydroxyl groups. The system is crashing from the begining of the equilibration step (after the following steps: vaccuum minimization, solvating, neutralizing, minimization, heating) due to -in all the replicas-