Re: [AMBER] help in amber

From: Jason Swails <>
Date: Wed, 8 Jul 2015 09:13:46 -0400

On Wed, Jul 8, 2015 at 5:31 AM, Robin Jain <> wrote:

> Dear all,
> i have simulate a organic molecule in 128 methanol in a cubic box of 21
> angstrom and after 60ns production , i want to use final coordinate for
> abinitio md, Therefore i load my trajectory in VMD to save last frame
> coordinates but after loading i saw that all the methanol molecules are too
> much far away from each other and their coordinates are out of box, for
> this i used another option given in Amber program such as ambpdb to save
> coordinates but it also show to much variable coordinates , specially in
> negative values. What is going wrong, Please help me in this regard.

‚ÄčThis is natural -- you would expect individual solvent molecules to drift
out of the unit cell from which they started. But keep in mind that with
periodic boundary conditions, when a particle drifts out of a particular
unit cell, another of its periodic images drifts in on the opposite side.

This is simply a visualization artifact caused by the fact that we only
store the positions of *one* image of each particle (it's impossible to
store all infinity of them, obviously). You can use the "autoimage"
command in cpptraj to map everything back into a single unit cell if this

trajin your_trajectory
trajout imaged_trajectory

Obviously change the names of the trajectory files to what you want.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 08 2015 - 06:30:03 PDT
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