Re: [AMBER] Change simulation box size

From: David A Case <>
Date: Wed, 6 Feb 2019 10:59:00 -0500

On Wed, Feb 06, 2019, Anthony Cruz-Balberdy wrote:
>I'm trying to simulate the aggregation of 300 small molecules into a
>nanostructure. I started the simulation with simulation box big enough so
>that the molecules were not too close together. During the simulation, the
>molecules started to aggregate and started forming the nanostructure that I
>was expecting. The only problem is that the nanostructure is open in the
>middle because the top part of the structure is touching the top of the box
>and the bottom part of the structure is touching the bottom of the box
>(along the z-axis). I think that if the box size change along the z-axis,
>the nanostructure will be able to close itself.

Are you sure this is not an imaging problem? Try playing with the image
command in cpptraj to see if you can just change the location of the
unit cell boundaries to get what you want.


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Received on Wed Feb 06 2019 - 08:00:02 PST
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