[gmx-users] PBC - Protein and Ligands
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 29 18:18:20 CET 2012
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,
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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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