[gmx-users] Remove PDB and center the protein.

Florent Hédin work at fhedin.com
Tue Aug 23 09:39:02 CEST 2016


I did something similar last month for a protein tetramer solvated using
a truncated dodecahedron ;) Hope the following will help

gmx trjconv -s inp.tpr -f inp.xtc -o clust.xtc -center -pbc clust

gmx trjconv -s inp.tpr -f clust.xtc -o ok.xtc -center -pbc mol -ur compact

As simulating a tetramer the key in my case was to use clust in the
first step for pbc, otherwise I was also not able of properly centring
the whole protein system.

I don't know if it is useful to use center twice by hte way ; may be
gromacs experts will know more.



On 23/08/16 08:42, dipak sanap wrote:
> HI all,
> I have simulated protein in a dodecahedron box. I know trjconv can be used
> to center the protein and remove PBC but I am confused.
> I have tried few cases as follows.
> Case 1
> trjconv -f *.xtc -s *.tpr -center -o centered.xtc
> trjconv -f centered.xtc -s *.tpr -pbc mol -ur compact -o centered_noPBC.xtc
> Case 2
> trjconv -f *.xtc -s *.tpr -pbc mol -ur compact -o noPBC.xtc
> trjconv -f noPBC.xtc -s *.tpr -center -o centered_noPBC.xtc
> Case 3
> trjconv -f *.xtc -s *.tpr -pbc mol -ur compact  -center -o
> centered_noPBC.xtc
> In all cases, I use protein for centering and system for output. Only third
> case keeps protein in center without jumping. What is the best way to
> correct trajectory for both visualization and analysis?
> Regards,
> Dipak

Florent Hédin
work at fhedin.com <mailto:work at fhedin.com>
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