Hi , I am a beginner in gromacs. I have made some topology files for graphene sheet with different bonded and non-bonded parameters I found in the literature. Now, how can I choose the best typology based on the energy minimization results? Can the lower maximum force on atoms or lower final potential energy determine which topology is the best? Or is there any other analysis that shows the validity of the defined topology?
Thank you in advance.
I haven't simulated graphene, so take this with a grain of salt.
I don't think you can use the EM step for topology selection. I imagine you would have to run some actual simulations (NPT, NVT, MD) and then analyse the MD simulation to see if the properties you are observing are reasonable based on experiments. You would also need to know what the "normal" is for what you will be measuring in the simulation
Hi, you shouldn't give too much attention here to the energy minimization. In principle, one does the energy minimization for getting rid of bad contacts or bad configurations in general. Highly likely, you won't ever reach any global minimum with configurations. So using the energy minimization for selecting the topology is the wrong thing to do. If you want to run MD and see what system you'll get in the end, then do it.
Thank you John and Inna. Now would you please suggest a routine analysis after MD simulation for graphene sheet which shows the validity of the defined topology? In fact, graphene is one part of my system and it is the first step to only check if its topology is Ok.
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