[gmx-users] how to set the number behind "d"in "editconf"

[Mark Abraham]

willting wrote:
> Dear all,
> 
> When I use the command "editconf ",I don't know how to set the number 
> behind "d".
> For example of /share/tutor/speptide,the number is 0.5,how to calculate 
> it ?

As you'd see from editconf -h, it's the distance from your solute to the 
box you're creating. You need this at least as large as your longest 
cutoff in order to implement the minimum-image convention, and you 
should look at the recent literature for the sort of simulation you're 
doing for some clues on how large people think you should be using. This 
choice will strongly influence the cost and accuracy of your simulation.

Mark