The box size determined for my protein before starting the MD simulation is as in image 1. After 200 ns, some of the protein comes out of the box (image 2). Does this affect the simulation negatively? I see that the build is not balanced (image3). Should I extend the simulation with this box size or repeat the simulation by changing my box size? What are your suggestions?
Dear Berna Erdoğdu
There seem to be two separate issues.
(i) The protein coming out of the box is not really a problem. Please take a look at periodic boundary conditions (PBC) and how they work. The protein is not really out of the box. You can turn on PBC representation when visualising the trajectory.
(ii) The box is likely to be very small with respect to the protein you are simulating. If you take into account PBC, then in the second image you post the protein is basically interacting with itself (you will see it very clearly if you turn on PBC representation). You should use a much larger sim box to avoid self-interaction, which will give rise to numerical artifacts.
Best,
Nicola
You can use the cubic box instead of dodecahedron while defining the unit cell. it may work
- Badges
- Science topic