[gmx-users] Umbrella Sampling between Nanotubes

Dr. Vitaly Chaban vvchaban at gmail.com
Mon Feb 17 14:47:49 CET 2014

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.neumann08 at 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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