This problem has been a bane of my existence for the last month.
This is one where it felt like there could be a lot of red herrings and there were that led me into different paths. As you may refer to my poster: Balancing Van Der Waals Force I am mixing solvents.
Well during equilibration the energy exchange between component A and component B is spiking really high causing a system explosion. The tolerance exceeded means it passed it’s threshold running at NPT to maintain constant pressure. It’s an unstable mixture.
If I look at the hydrogen distance between two molecules. I get around 2.298 angstroms. I’m assuming that this energy change
This is not the average of the H-H contacts but rather just one representation. I believe what is going on is that when I create the system of both components I am placing the molecules too close with each other.
Steps to fix for our particular system.
- Check to distances between molecules on initial setup. Place the molecules in an offset from each other before minimization:
calc deltay ((@j * @xlatxa) + (0.5 * @xlatxa))
calc deltaz ((@k * @xlatxa) + (0.5 * @xlatxa))2. Make the box and subsequent boxes larger, run your equilibration longer and allow the system to relax.
