Re: [AMBER] problem in amber

From: Jason Swails <>
Date: Thu, 9 Jul 2015 07:52:00 -0400

On Thu, Jul 9, 2015 at 3:32 AM, Robin Jain <> wrote:

> Dear all.
> I have simulated my molecule in a cubic box of 20.61 A using periodic
> boundary condition. After a 60ns run the last line in restart file show
> the cell size 20.95 A. Now i want to do a abinito md using cpmd , for this
> i got a pdb from last trajectory and then convert it into .xyz file and
> then upload into molden to create a cpmd input which show the cell size
> 25.04 A,
> 1. why the cell size difference come in classical md and in abinitio md?

There *is* no difference. Or, rather, there shouldn't be. How is molden
defining the box, do you know? If it simply defines a box that encloses
the centers of every atom (which I suspect is the case), then the periodic
box is *actually* too large. When Amber images, it puts the center of mass
of every molecule inside the same box, but that means that some atoms can
extend into adjacent boxes.

2. If i use 20.95 A cell size, the solvent molecules comes out the box in
> molden why, they do not come out in AMBER MD.

​Probably due to what I described above.

> 3. using 20.95 A cell size molden show very poor periodicity while using
> 25.04 A, it show good one. Why?

​I have no idea what this means.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 09 2015 - 05:00:03 PDT
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