[gmx-users] center the protein to the origin

[Justin A. Lemkul]

Asmaa Elsheshiny wrote:
> Hi, I am simulating a protein in water. But I have forgotten to center the
> protein from the beginning to the origin. So, is it possible to center the

When using periodic boundary conditions, the "center" of the system is an 
arbitrary designation.  Gromacs builds boxes from the origin, so even if you had 
centered the protein, it wouldn't have been at the origin.

> protein to the origin in the trajectory file? And if it is not possible, how

trjconv -boxcenter zero, if you really think you need to do this.

-Justin

> can  obtain the atomic positions independent of  the center of mass, to use
> for further analysis? Cheers, Asmaa


-- 
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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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