Comparison between two MD

User discussions
1

GROMACS version: 2020
GROMACS modification: No

Hi gmx users,
I did two simulations. 1) polymer(x)-drug and 2) polymer(y)-drug. In these two simulations, the polymers are different but the drugs are the same.
According to the structure and shape of the polymers, the size of the box is much larger in the second simulation. I want to know if I can compare the analyzes done for these two simulations? Is it logical?

2

Dear Lilian,
Yes, it’s perfectly fine to compare simulations even if your polymers have different sizes, but it of course depends a bit on what you want to study. Can you provide some more details about what you wish to do?