[gmx-users] tpr file

Justin Lemkul jalemkul at vt.edu
Tue Oct 16 15:34:03 CEST 2012

On 10/16/12 7:42 AM, ahmet yıldırım wrote:
> Hi,
> I converted a .tpr file to .pdb using editconf.
> editconf -f md.tpr -o new-md.pdb
> I visualised new-topol.pdb using pymol. It has the virtual sites.
> Furthermore, the molecule(s) does not stay in the centre of the box.
> I need a proper .tpr or .pdb file for analysis.
> How can these problems fixed?

The "center" of a periodic system (assuming that's what you have) is arbitrary. 
  If you need some fixed reference, that's what trjconv -center does.



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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