[AMBER] box size

From: Qinghua Liao <scorpio.liao.gmail.com>
Date: Fri, 1 Jun 2018 19:10:57 +0200

Hello everyone,

I am trying to set the water box size, but I failed to get what I want.

For example, I tried to put the protein in a water box with commands:

set mol box {160 160 160}
solvatebox mol TIP3PBOX 0.0

Then the box information I got is something like this:

   Solute vdw bounding box:              160.000 160.000 160.000
   Total bounding box for atom centers:  160.000 160.000 160.000
   Solvent unit box:                     18.774 18.774 18.774
   Total vdw box size:                   175.760 163.366 162.873 angstroms.
   Volume: 4676619.621 A^3

The box size is 175.760*163.366*162.873 A3, but not 160.0*160.0*160.0 A3
which is what I expected.
Could someone tell me how and why the new box size was generated? Thanks
a lot!

All the best,

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Received on Fri Jun 01 2018 - 10:30:02 PDT
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