[gmx-users] choosing box vectors

Justin Lemkul jalemkul at vt.edu
Sat Jun 15 02:09:57 CEST 2013

On 6/14/13 8:08 PM, gromacs query wrote:
> Dear Justin,
> I saw your tutorial (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
> )
> But my case is different. I can not even generate tpr file (trjconv as
> tutorial says) as it need box info
> Can you please suggest what can be the best possible way? If I just use
> system size dimension (X, Y Z) and do mimization it break my system in
> parts!
> How to choose optimum box vector in such case?

Omit "-bt cubic" from your command and it should work fine.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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