Re: [AMBER] Do molecular dynamics in the limited space

From: case <>
Date: Fri, 23 Apr 2010 08:50:32 -0400

On Fri, Apr 23, 2010, Yunjie Zhao wrote:

> The setBox command adds a periodic box to the UNIT. It does not add any
> solvent to the system. The solvateBox command creates a rectangular
> parallelepiped solvent box (explicit water) around the solute UNIT. It is
> the periodic box too.
> I want to do the molecular dynamics in the implicit water, such as igb5
> model. Is there any way to add only one box like a container with the
> container wall of 10 A?
> Thanks!
> > > I would like to do molecular dynamics in the limited space, such as in
> > > the rectangular box with "20*20*100" or in the cylinder with the diameter
> > > of 20 A.

If you mean that you want to *not* have periodic boundary conditions, but
rather a box with "walls" that molecules would hit if they moved very far:
Amber does not support such simulations.


AMBER mailing list
Received on Fri Apr 23 2010 - 06:00:17 PDT
Custom Search