[gmx-users] helping increasing box

[Giuseppe R Del Sorbo]

Dear all,

I am doing COM-pulling simulations between two lysine chains connected 
with a surfactant.

Basically I want to find the force able to separate the two chains.

Increasing the force, at some point gromacs was complaining that the 
distance between the two pull groups is larger that the half of the box 
lenght.

To solve this problem, I increased the box size but now the two lysine 
are not
connected anymore.

When I open with vmd the .gro file, the two chains are not connected but 
far away because, of course, I increased the box.

I should move the two chains at the end of the box. In this way when on 
VMD I add other boxes in +y and -y directions I will able to see the two 
chains connected and not separated from a gap dipending on the 
increasing of the box.

But I don't know how to do this.

Do you have any suggestion?

Thanks

Giuseppe