[gmx-users] -pbc nojump

[Mark Abraham]

On 20/10/2010 9:55 PM, leila karami wrote:
> Dear Mark
> my mean of [when I used trjconv -pbc nojump, I made one group (protein and dna) in index file and I selected that as centering group.] is that
>
> the problem (nonentity of water molecules in interface of protein and dna) was not solved.
>
> what is your mean of [You might need two passes with trjconv]?
You might need to use trjconv once to center, and then again to put all 
the molecules in the box (or similar). trjconv can't always do 
everything you want in one invocation.

Mark