[gmx-users] trjconv -pbc nojump -center rect => does not work

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
>  I have a protein+several ligand in the simulation box.
>  After 5ns, the protein drift to the right edge of the box and the
>  ligand drift to the left edge of the box.
> 
>  I am very sure that the ligand has attached to the protein.
> 
> 
>  with this command =>
>  trjconv -pbc nojump -center rect
> 

This is not a correct command; -center does not take an argument.  In any case, 
I have found that trjconv -pbc mol -ur compact -center (and choosing 'Protein' 
to be centered) works quite well.

-Justin

> 
> 
>  so, how can i use trjconv command to see protein-ligand complex as a whole?
> 
>  Thank you
>  Lin
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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