Chih-Ying Lin wrote:
Hi
1. in the last row of .gro file, the three number represent the length
of the box on X, Y , and Z directions in nanometer.
Right??
These values represents the real dimensions of the box
2. for the editconf command,
editconf -d Distance_between_the_solute_and_the_box bt cubicsur
Right??
In this case the program takes the solute and calculates the solvation
surface. From this calculates the maximum size of this surface, add
twice the value "Distance_between_the_solute_and_the_box" (distance in
the left side and distance in the right side), and the total value is,
in the case of cubic box, the size of each direction of the box (X=Y=Z).
Some careful reading of the Manual will help.
what are the differences between the three number in the .gro file and
the distance in the editconf command ??
Thanks
Lin
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