[gmx-users] Protein coming out of the box

[gtroiano at if.usp.br]

 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?

 Thanks in advance,
 Gustavo


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