# [AMBER] How the box info is used

From: Ilyas Yildirim <i-yildirim.northwestern.edu>
Date: Wed, 3 Nov 2010 16:54:24 -0500 (CDT)

Dear Amber users,

I am trying to create a rectangular cuboid system and end up having
vacuum bubbles while heating the system up to 300 K. I am thinking that
the problem is with the box info I manually enter to the inpcrd file.
Therefore, I want to understand how sander/pmemd does reading of box
information while doing the calculations. I have a couple of questions and
will appreciate any response. Thanks in advance.

1. After creating the inpcrd file using 'setbox mol centers', the last
line in inpcrd file is

61.3200000 59.8490000 68.9990000 90.0000000 90.0000000 90.0000000

When I check out the .pdb file that was used to create the inpcrd/prmtop
files, the minimum and maximum x,y,z coordinates/points are (0.137,61.457)
for x, (-0.099,59.750) for y, and (0.016,69.015) for z. How does the
program understand how to put the cells next to each other? Also, when the
simulation is run, the water molecules fly to the neighbouring cells, and
let's say I have that .rst file at hand. When I try to put the atoms in
this .rst file into the primary cell/box, how does the program do the
calculation? Is there a reference point the program calculates before
putting the atoms into the primary cell?

2.In the above inpcrd file, delta(x) is 61.457-0.137=61.320 (max_x -
min_x), which is the length of the x-axis in the rectangular cuboid. The
same is true for y and z; delta(y) and delta(z) are exactly equal to
59.849 and 68.999.

If the first atom in the .pdb file has the (x,y,z) coordinates of (0.137,
-0.099,64.247), is one of the images in the neighboring cell will have a
coordinate of (0.137+61.3200000, -0.099,64.247)? If yes, will the
images of the rest of the atoms be created the same way?

3. The system that I prepared has 2 surfaces/planes (top, bottom) that are
filled with water+ions in between and the whole system looks like
rectangular cuboid. The surfaces/planes are not PURE rectangular cuboids,
however. Yet they can repeat on x,y,z axis when the right delta(x),
delta(y) and delta(z) is used. For instance, in VMD, when I set the box
information as a=61.32, b=60.69106, c=71.38317, and alpha=beta=gamma=90,
and look at the periodic cells, I see the right repetition of the
surfaces/planes on x,y,z axis. Can I use these a,b,c values and replace
the last line of inpcrd with these ones?

Ilyas Yildirim, Ph.D.
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= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
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Received on Wed Nov 03 2010 - 15:00:03 PDT
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