Hello everyone,

I have built a mixture containing 12 kinds of molecules with initial density of 0.1g/cm3 to make it a large box. After geometry optimization, NVT run is performed to pre-equilibrate the system in Forcite module. Then NPT run under same temperature is applied to the last frame of trajectory to approach a stable state.

I want to analyze aggregation for a fraction in the system, and this fraction is composed of 5 molecule A, 4 molecule B and 5 molecule C. RDF (radial distribution function) is used to achieve this. I create a set D containing all molecules A, B and C. Then RDF of set D is calculated for both NVT and NPT runs. Strangely, after NVT run, RDF curve of first several frames is higher than that of subsequent frames, and much higher than RDF in NPT run, as shown in the following figure.

I’m wondering why this happens. I have thought that RDF would increase with the equilibration and compression of model box because molecules become closer to each other.

Can anyone tell me the reason?

By the way, here is another question: how to obtain density for a set? I can only get system density through Forcite analysis.

I wish that someone can help me. Thank you very much.