[gmx-users] PBC - Protein - ligand

Steven Neumann 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?

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111107/dec8e588/attachment.html>

More information about the gromacs.org_gmx-users mailing list