[gmx-users] On the box type

[akcyrus]

Dear all,
The only tutorial on umbrella sampling by Justin (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html)
assumes a rectangular box and pulling is done to separate chains. Is it
true that the approach worked solely because one of the reference chains
was position restrained as that did not allow it to rotate.
regards,
cyrus


On Sun, Jul 7, 2013 at 4:45 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Sun, Jul 7, 2013 at 4:15 PM, akcyrus <akcyrus at gmail.com> wrote:
> > Dear all and Tsjerk Wassenar,
> > I could not grasp how a rectangular box will be a problem. Lets assume a
> I
> > have a cylinder of radius r (nm) and height h (nm) with h>r. I place the
> > cylinder aligned along z-axis and then in a rectangular box with
> dimension
> > 2r+2.0 nm, 2r+2.0 nm and 2h+2.0 nm. My understanding is that the problem
> > could be when during simulation, the cylinder gets aligned parallel to XY
> > plane and the box vectors are shorter along X and Y,isn't that right?
>
> Yes. If that can happen, then your simulation will become junk when it
> does.
>
> > Also
> > during the simulation, with isotropic pressure coupling the box tend to
> be
> > cubic and this would also cause problems. Correct me if I am wrong or
> don't
> > understand it right.
>
> Anisotropic coupling is available. But I don't think that is an issue
> in choosing whether a rectangular box is plausible.
>
> Mark
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