[gmx-users] Non Periodic Coordinate File

[ANAND AMITKUMAR Dharia]

Wow, thank you so much, don't know how I didn't realize this.


On Thu, Aug 20, 2015 at 3:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/20/15 5:59 PM, ANAND AMITKUMAR Dharia wrote:
>
>> Hello,
>>
>> I was wondering if it was possible to create a non-periodic coordinate
>> file
>> using trjconv or some other gromacs program on a trajectory file. I would
>> like to use coordinate data to calculate displacement in order to compute
>> a
>> crosscorrelation between molecules, however, with the jumps in the
>> coordinate file, there is no meaningful result. I understand I can use the
>> -ur pbc mol command, but this just makes the molecule whole before
>> bouncing
>> across the screen. Any input would be helpful.
>>
>>
> trjconv -pbc nojump
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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