[gmx-users] trjconv with multiple chains problem

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 7 03:29:59 CET 2011

yuanyuan wang wrote:
> dear all,
>          I am doing a simulation that have many chains in a box , and I 
> can find a center for them after serval tries.
>          I use almost every option of trjconv,-pbc 
> mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger 
> box, and -boxcenter, -fit ..
>          still some chain cannot convert into box. them jump from one 
> box to another ,
>          is there any ways that they not jump to another box?
>          thanks a lot.

Use a custom index group to center on some subset of atoms that you want to be 
centered in the system.  If you try to just center on, for example, "Protein," 
the geometric center may lie in the middle of the unit cell but the chains are 
split across periodic boundaries.


> yuanyuan


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


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