[gmx-users] PBC - Protein and Ligands

[Justin A. Lemkul]

Steven Neumann wrote:
> Dear Gmx Users,
>  
> I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. 
> The problem I face is PBC which I cannot get rid of. I used:
>  
> 
> 1.      First make your molecules whole if you want them whole (system).
> 
> trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc
> 
> 2.      Cluster your molecules/particles if you want them clustered
> 
>  
> 
> 3.      Extract the first frame from the trajectory as reference for 
> removing jumps if you want to remove jumps.
> 
> trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb
> 
> 4.      Remove jumps if you want to have them removed using the first 
> frame (system)
> 
> trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc
> 
>  
> 
> So the trajecory of my ligands is smooth but they do do bind to the 
> different periodic images. As i know it is impossible to obtain the 
> proper trajectory of all of them I just want to obtain the realistic 
> final positions of my system to extract pdb file for further umbrella 
> sampling. Any suggestions?
> 
>  

If you have a single protein to which all the molecules bind, you can simply:

trjconv -s md298.tpr -f md298SKIP4.xtc -o center.xtc -center (center on protein, 
output system)

trjconv -s md298.tpr -f center.xtc -o fit.xtc -fit rot+trans

The protein will stay in the center of the box, with its rotational and 
translational motions fitted.  It should produce a very smooth trajectory.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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