[gmx-users] gmx trjconv -center not working?
jalemkul at vt.edu
Fri Feb 8 13:39:07 CET 2019
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.
> On Fri, 8 Feb 2019, 5:27 pm Justin Lemkul <jalemkul at 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 A. Lemkul, Ph.D.
>> Assistant Professor
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Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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