[gmx-users] PBC - Protein - ligand
s.neumann08 at gmail.com
Mon Nov 7 15:08:02 CET 2011
Dear Gmx Users,
I know that this problem has been discussed may times but I cannot find the
solution to get rid of pbc in my system: protein and ligand. I followed the
1. First make your molecules whole if you want them whole
trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.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 mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
4. Remove jumps if you want to have them removed using the first frame
trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc
5. Center your system using some criterion. Doing so shifts the
system, so don't use trjconv -pbc nojump after this step.
trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc
6. Put everything in some box.
trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc
7. Fit if desired and don't use any PBC related option afterwards.
trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o
I used SYSTEM everywhere as output orinput. However, my ligand is still
jumping like a fly around the stable protein. Do you have any suggestions?
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