GROMACS version: 2022.3
GROMACS modification: No
Hi everyone,
I have a system with a protein and a ligand, and the result of the minimization step it’s the one in the image. After the minimization step, I usually obtain a structure that is not as strange as this one but it’s usually similar to the normal structure of the protein. I was wondering, is it ok a result like this or it’s a result of a problematic minimization step? Because if I run again the minimization with the same input files I obtain a protein that is similar to the starting structure and it doesn’t have that strange appearance.
In the past, I had a minimized structure like that only in one situation where I had several warning messages during the minimization step but in the current simulation I don’t obtain any warning or anything strange. I checked again in the log file too and I don’t see anything weird. Please let me know what could be. Thank you very much!
Martina
Hi Martina!
I don’t quite understand what you mean by your minimized structure being “strange”. Is it because your protein is covering the edges of the periodic box and therefore the visualization looks a bit strange? If you don’t get any warnings or error messages, there’s probably nothing wrong. However, it’s always a good idea to inspect the structure after minimization. If you want to remove the PBCs (for visualization only) you can use trjconv (https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html).
Sorry, I’m quite new to mds and this doubt came to my mind. Yes, I was thinking about the visualization that looks a bit strange, I was looking for a confirm about the fact that if I don’t get any warning message so it’s everything ok and I just need to remove the periodic boundary condition for visualizing the protein. So, thank you very much!
The fact that the protein appears split over periodic boundaries is no problem, but the huge solvent void present suggests you did not add enough water into the system and it will be unstable.
Yes actually in that image, not all the water molecules were shown, the real situation is represented in this second image so I think there are enough water molecules but thank you, I had never thought about the possibility of not adding enough water molecules for the stability of the system.
