[gmx-users] Umbrella Sampling between Nanotubes

[Steven Neumann]

Thanks for this! That makes it challenging with a system with more
nanotubes then... so I will start with two.
Have you ever tried to apply umbrella sampling to caluclate the PMF? Do you
think it is the best way? I just want to define the equilibrium distance
between two nanotube surfaces... And also if you use it which options in
mdp would you recommend:
pull-geometry: distance of cylinder?
pull: umbrella?

I have some polypeptides attached to my both nanotubes, would the specify
the index groups as nanotubes only or both nanotube+polypeptide
(pull-group0 and pull-group1)?

Thanks a lot,

Steven



On Mon, Feb 17, 2014 at 1:47 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> 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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