[gmx-users] problem with the translate option of editconf

[Justin A. Lemkul]

Ozge Engin wrote:
> Hi all,
> 
> I am trying to translate the peptide within the simulation box. I have a 
> box with dimensions of 3.8 3.0 3.0 nm^3, and I want to put the peptide 
> on top of the box. In order to that I used the following command line:
> 
> editconf -f pep.pdb -box 3.8 3.0 3.0 -translate 0 0 1.5 -o trans.pdb
> 
> The peptide is not translated, but sitting at the center of the box. Why 
> is the case? Any suggestions?

The use of -box implies -c, so either use -noc or set the center explicitly with 
-center instead of -translate.

-Justin

> 
> Thanks in advance
> 
> -- 
> Ozge Engin
> ★☆
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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