[gmx-users] How to center molecules in the box with trjconj ?

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 20 19:19:23 CEST 2010

ABEL Stephane 175950 wrote:
> Hi all,
> I have simulated a system containing 55 DPC molecules, a peptide some ions
> and water in a cubic box. Initially all molecules were placed randomly in the
> box. As expected during the simulation all the DPC molecules aggregate to
> form a stable micelle with the peptide located at the micelle interface.
> Now I would like to plot some MD configs in a PDB format some configs where
> the micelle and the peptide are placed in the center of the box. To take into
> account the PBC and to obtain the PDB, for the last frame at 150 ns as I used
> trjconv with the following commands:
> 1-  trjconv_mpi -f traj_KTM17_DPC_all.xtc -s hMRP1_K-TM17_DPC.tpr -pbc nojump
> -b 150000 -e 150000 -o traj_KTM17_DPC_0ns_noJump.pdb
> With "non-SOL" (DPC and peptide) as a group for output and where
> traj_KTM17_DPC_all.xtc is the trajectory with *no* PBC transformation
> 2-  trjconv_mpi -f traj_KTM17_DPC_0ns_noJump.pdb -s hMRP1_K-TM17_dpc.gro
> -center -o traj_KTM17_DPC_0ns_noJump_center.pdb
> With DPC as a group for centering and "System" (DPC and peptide) as a group
> for output. the *.gro file contains only the DPC and peptide.
> Unfortunately, these commands do not work since the micelle (and the peptide)
> are not in the box center. I have tried many others commands with -pbc as
> mol, res with no success.

I have never had much success using multi-molecule groups for centering or other 
correction using trjconv.  Centering on the peptide, i.e. trjconv -pbc mol -ur 
compact -center, should do the trick.  I have never found -pbc nojump to work 
very well, for a reason that is still unknown to me.


> I used GMX version 4.0.7
> Any advices would be helpful.
> Stefane


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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