[gmx-users] tpr file

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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