[gmx-users] trjconv -pbc -center

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 19 02:16:19 CEST 2009

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 supposed that the ligands
> dock/attach on the protein.
> I want to center the protein and see if the ligands dock/attach on the protein.
> The command trjconv is used.
> I have tried different option -pbc and -center.
> Even though I center the protein, but the ligand is still away from the protein.
> It seems not make sense.
> with option -pbc cluster
> the computer was running and never end.
> so, how can i use trjconv command to center protein and to see the
> ligand attaching on the protein?

Well, does the association you expect actually occur?  It seems to me that if 
you center the protein in the box, and the ligands do not associate, then you 
can't force it to happen with trjconv.


> Thank you
> Lin
> Option -pbc sets the type of periodic boundary condition treatment:
> * mol puts the center of mass of molecules in the box.
> * res puts the center of mass of residues in the box.
> * atom puts all the atoms in the box.
> * nojump checks if atoms jump across the box and then puts them back.
> * cluster clusters all the atoms in the selected index such that they are all
> closest to the center of mass of the cluster which is iteratively updated.
> Note that this will only give meaningful results if you in fact have a
> cluster. Luckily that can be checked afterwards using a trajectory viewer.
> Note also that if your molecules are broken this will not work either.
> * whole only makes broken molecules whole.
> Option -center centers the system in the box. The user can select the group
> which is used to determine the geometrical center. The location of the center
> is set with -boxcenter: tric: half of the sum of the box vectors, rect: half
> of the box diagonal, zero: zero. Use option -pbc mol in addition to -center
> when you want all molecules in the box after the centering.
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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


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