Re: [AMBER] box size

From: David A Case <>
Date: Sat, 2 Jun 2018 07:39:08 -0500

On Fri, Jun 01, 2018, Qinghua Liao wrote:
> Thanks a lot for your explanation! I am still a little confused here.
> Since 0 padding was added by solvatebox, I am not sure how the total vdw
> box size
> is being different from the solute box dimension.
> Then, how should I get a exact box size what I want, trial and editing
> the coordinates file? Thanks a lot!

If you need to pre-set the box size, you can use the AddToBox command,
but this requires knowing (often by trial and error again) how many
water molecules to add. AddToBox is primarily pointed towards crystal
simulations. If you need an exact box size for a solution simulation,
you can use trial and error with solvateBox, or take a look at packmol.
I am personally not very familiar with the latter, but a version of this
code is now included in AmberTools18.

For all of these, remember that the initial box size will change as you
do NPT equilibration, which is required to get a good description of the
water environment. So you might want to think about whether the need
for a specific box size is really crucial.

...good luck....dac

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Received on Sat Jun 02 2018 - 06:00:03 PDT
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