[gmx-users] box size

Nuno Azoia nazoia at det.uminho.pt
Fri Jul 4 11:33:31 CEST 2008

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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Nuno Gonçalo Azoia Lopes

Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
Universidade do Minho
Campus de Azurém
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E-mail: nazoia at det.uminho.pt

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