[gmx-users] PBC - Protein and Ligands

[lina]

On 1 Mar, 2012, at 1:01, Steven Neumann <s.neumann08 at gmail.com> 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?

You may wanna try 

Trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -ur compact -o pdbs.pdb -dt 1000

Please change dt if necessary. 


>  
> Steven
>  
> -- 
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