[gmx-users] PROTEIN FOLDING

[Justin Lemkul]

On 12/28/17 8:33 AM, Neha Gupta wrote:
> Hi,
>
> I tried this one
>
> gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n
> index.ndx
>
> This asks me to select a group fro clustering and then select a group for
> output..
>
> What should I select first and then next?

Clustering isn't relevant. Your situation is much simpler than it's 
being made out to be.

1. Make molecules whole
2. Remove jumps
3. Center

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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