[gmx-users] PBC - Protein and Ligands

[Steven Neumann]

Thank you all! That helped a lot!

Steven

On Wed, Feb 29, 2012 at 5:17 PM, Vedat Durmaz <durmaz at zib.de> wrote:

> **
> i always did it (successfully) with one single command:
>
> trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n
> ../../index.ndx
>
>
> regards
> vedat
>
>
> Am 29.02.2012 18:01, schrieb Steven Neumann:
>
> 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?
>
>
>
> Steven
>
>
>
>
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