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

From: Yunjie Zhao <>
Date: Fri, 23 Apr 2010 10:35:10 +0800

Thanks a lot for your quick and right answer.
  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?

Yunjie Zhao

2010/4/22 Bill Ross <>

> > 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.
> Cylindrical space is not supported.
> Usually when there is a box, there is also a solvent, usually water.
> The solvateBox command will build a box to enclose a given radius
> from the solute. However the size will not be exact, and the radius
> will be observed the same in eacxh dimension. Then the system must
> be equilibrated at constant pressure to make the density correct.
> See the demos for details.
> If you want a molecule in vacuum in a box, you can try 'help setbox'
> to see how to create a box, then after saveamberparm you can edit the
> prmtop and inpcrd to expand the box to the dimensions you like.
> Bill
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Received on Thu Apr 22 2010 - 20:00:03 PDT
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