[gmx-users] gmx trjconv -center not working?

[Justin Lemkul]

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 <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
>>
>> --
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>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
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
http://www.thelemkullab.com

==================================================