Hi all I'm simulating a helical protein in a water box, neutralized with Na and Cl to a 0.2M comcentration. I had to pick the smallest box I could (in editconf, rectangular, with -d 0.1, and -princ to align the box with the helix). But in the MD trajectory I see the protein coming out of the box, most of the time. I know that it uses PBC, and I'm seeing just 1 image, but does it mean that there's something wrong with the MD?
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