On 2/8/19 7:22 AM, Rajat Desikan wrote:
Hi Justin,
"A cubic box is already as compact as it can be."
That's true and I understand that :) it's just that I have faced similar
issues with trjconv that Mala appears to be grappling with, and this
combination has always resolves it for me. I don't know why. I can attach
test files that show this behavior.
If the box is non-rectangular, then -pbc mol -ur compact may help, but
that combination simply makes molecules whole and re-wraps the box so
that it takes its true shape. With a cubic box, it will do nothing, and
was merely pointing that out for the sake of anyone who comes across
this thread in the future.
-Justin
Rajat
On Fri, 8 Feb 2019, 5:27 pm Justin Lemkul <jalem...@vt.edu wrote:
On 2/8/19 5:17 AM, Rajat Desikan wrote:
Hi Mala,
Please combine -center with "-pbc mol -ur compact" and check.
Compact unit cell representation is only useful for dodecahedral and
octahedral boxes. A cubic box is already as compact as it can be.
-Justin
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