Dear Friends I have run a simple self-assembly simulation of a lipid bilayer. When I look at the trajectory, the bilayer normal is aligned along the y-axis, and the bilayer is not centered to the middle of the box, but towards the edge of the box. So, the bilayer is split into its periodic image. I was wondering what would be a good way to center the bilayer in the middle, and perhaps align it along the y-axis too? I know this can be done for a single .gro file using editconf, but how does one to it for a trajectory. I have tried various combinations of -center (zero, rect, tric) and -fit (trans, rot+trans), but nothing seems to work perfectly. I am using 3.3.1
Thanking you -Maria -- Maria G. Technical University of Denmark Copenhagen
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