[AMBER] Change simulation box size

From: Anthony Cruz-Balberdy <anthonycruzpr.gmail.com>
Date: Wed, 6 Feb 2019 08:24:24 -0500

Hello everyone,

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.

There is any way to change the box dimensions to allow the nanostructure to
close itself?
Could this be achieved by changing the pressure regulation from isotropic
to anisotropic?
Should I change the simulation box dimensions manually by slowly decreasing
the box size along the z-axis while increasing the size along the x- and

Any help would be greatly appreciated.


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Received on Wed Feb 06 2019 - 05:30:01 PST
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