If we want to study some systems, for example chemical reactions, we do better to use the non-PBC conditions. Why? Because generally we need use the radius of gyration in the PLUMED manual. Here I imply we should use biased AIMD, i.e. metadynamics.
If you use the radius of gyration, you should realize this method is not appropriate for PBC condition (read the PLUMED manual). However, if you use the non-PBC condition, you have to worry about the fragments or radicals such as hydrogen atoms could fly away and cross the box boundaries. This crossing could cause bad problems for AIMD simulations because you will have nonphysical results.
So another suggestion is that you should add more constraints such as harmonic potential on every individual hydrogen atom and mass center of the whole system. This way you can make sure the lightest fragments fly away.
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