GROMACS version: 2025
I was told to follow a research paper’s protocol and build a 10M urea osmolyte box. I have successfully completed it, but I have a doubt about how to calculate h value, when I am using gmx energy command, there are 2 values for average energy prompted ; Potential energy and total energy. If I am calculating by Potential energy h value is coming around 1.5 while using total energy it is equal to 4. Which one shall i opt for? And also I performed the simulations using CHARMM force field and AMBER and in both cases NVT values are almost same.
Please share your insights. Thank you.