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Hi there, I am simulating a protein-DNA complex with a 70 bp long DNA. For this purpose I am trying to define the box size, but my DNA is sticking out of the system if I do not chose d = 10.0 which makes the systems extremly large and simulation very slow. So my question is, if it causes problems if the DNA is sticking out of the system even if Periodic boundary conditions are applied?
Thanks a lot in advance!
There is no such thing as “outside” a periodic box. With editconf -d there will be a suitable buffer around your system; if it appears as if something is “outside” the box, I assume you’re using a non-cubic box (like a rhombic dodecahedron) and the issue is just that you are looking at a triclinic representation of it (the default in all GROMACS tools) and you need to eventually re-wrap it with trjconv -pbc mol -ur compact after you have generated a .tpr file for some process (minimization or dynamics).
ah okay thank you !
good to know