Dear community,
I have been trying to model PMP membranes with a nanoparticle using the martini forcefield in GROMACS. At first all the md simulations were going well, however when we started using from Simulated Annealing to standardize our initial conditions, we started receiving the error:
The total potential energy is nan, which is not finite. The LJ and electrostatic contributions to the energy are 0 and 0, respectively. A non-finite potential energy can be caused by overlapping interactions in bonded interactions or very large or Nan coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology.
This seems to indicated that particles were moving too far for the conditions set so the team wanted to increase the r conditions to a greater value (rvdw and rcoulomb), which did remove the error. However, the team also acknowledges that Martini parameters are supposed to be around 1.2 and not the 1.8 that we were using. Does anyone have any suggestions on what we should use for our rvdw and rcoulomb and if there are any other solutions to our error that we might have not considered?
We have tried with various r values, however as we increase it the density keeps increasing without leveling, raising some concern with our team. This phenomenon was not very expected for the Lennard Jones Potential part of the deal, maybe the increase is due to Coulomb potential? We are trying some atomistic solutions to compare with our model, but we are not yet confident on their results either.
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