I have built a membrane system using charmm gui. How can I know that the system is equilibrated after doing the equilibration steps? What are the values I should monitor to know?
Zhaoxi Sun thank you. But are not there some special properties for membrane system that indicates the equilibration of the system? or are the properties you mentioned enough?
How?: if you are using GROMACS, the gmx energy tool will help you make plots of temperature, pressure and etc … from the plots, the equilibration status could be inferred.
Martin Klvana I have calculated the area per lipid for one of the lipids (cholesterol) in the membrane. However, how can i know that this value is near the true area per lipid?
"The average area per lipid was calculated by multiplying the x/y dimensions of the simulation box and divided by the number of lipid and cholesterol molecules present in one leaflet of the bilayer."