[gmx-users] Umbrella Sampling between Nanotubes

[Steven Neumann]

Dear Gmx Users,

I am trying to setup the system of nanotubes with attached polypeptides. I
wish to define the equlibrium distance (PMF minima) between them. However
in my system, I will have 6 of them in which one is in its quarter in the
rectangular each box edge copied across pbc. It is the only one way I can
do this as 3 nanotubes form a isosceles triangle. However if I will change
the distance between them, I need to change the box size. Is that possible
to use in Umrella Sampling with the box which difer in number of atoms and
box size?

Or would you rather run first 1) run just 2 nanotubes - one with position
restraints and one with harmonic potential, evaluate PMF using umbrella
sampling (or sth else?) at different distances and then apply it with a
second system 2) made of more of nanotubes to with the distance defined from
 step 1)?

Please, advise

Steven