[gmx-users] Box dimension

rose rahmani rose.rhmn93 at gmail.com
Mon Jun 4 08:53:54 CEST 2018


I want to do umbrella sampling for different coordination of amino acid
through different distances (in Z dimension) from nanotube. The nanotube
axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
(because the nanotube radius is 0.65nm). The initial distance of amino acid
from nanotube is 2nm. The question is how should i choose the box Z
dimension that some artifacts (justin explained in tutorial) doesn't
happen? I choose 7nm, is it ok or large?

Would you please help me?

Best regards

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