Re: [AMBER] periodic box size

From: Rui Chen <>
Date: Fri, 30 Aug 2019 09:42:13 -0600


Thank you, I found the box size and centre. The box generated by tleap
includes a buffer layer, it's size is bigger than the true box size. Based
on my understanding, the total bounding box for atom centers
 is the real size that encloses all atom centers in the target box, the total
vdw box size adds a buffer region roughly equivalent to the vdW radius of
each atom near the boundary. Which one should I use as the periodic box
size? I think, no matter which one I use, the centre of the box is the
same, which I can find in coordinate file. Is that correct?

Best regards,

On Fri, Aug 30, 2019 at 5:31 AM David A Case <> wrote:

> On Thu, Aug 29, 2019, Rui Chen wrote:
> >
> >I am running MD simulation with NAMD, I prepare the protein (solvation,
> >ionization, making S-S bonds, connect glycans and ASN) using tleap. I'd
> >like to get the periodic box size.
> Look at the last line of the "inpcrd" file you created in the
> saveAmberParm command.
> ....dac
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Received on Fri Aug 30 2019 - 09:00:02 PDT
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