Not sure that I got your question correctly...
The atom indices, which you supply to umbrella code, can be defined as
you like, without being bound to the molecules they belong to in the
topology files. Therefore, if you need to restraint certain number of
atoms in a system, just enumerate them within the same index group and
supply the group name to the umbrella code.
Of course, if your aim is to compute free energies, all the involved
subsystems should be of the same composition.
Dr. Vitaly V. Chaban
On Mon, Feb 17, 2014 at 9:38 AM, Steven Neumann s.neuman...@gmail.com wrote:
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
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