GROMACS version:2020.03
GROMACS modification: No
Dear experts,
When I was doing the steered molecular dynamics, I added the terahertz electric field (in the .mdp of SMD) to the RNA system. I found that when the electric field within 4-16 THz was added, the water box expanded (the first gif is the water box expansion at 8 THz), and the distribution of water molecules in the expanded part was uneven (like the second gif).
At other frequencies, such as 22-45 THz, this is not the case. The temperature and pressure of the stretching process are stable (v-rescale temperature coupling and Parrinello-Rahman pressure coupling), the size of the water box does not change, the distribution of water molecules is uniform, and all the analyses are correct. I have checked the parameters and there is no problem. I want to ask why the expanding part of the water molecules is not evenly distributed or is it the software itself?
