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
--
========================================
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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