Steven Neumann wrote:
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 workflow:
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
mdfinal.xtc
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?
Center on either the protein, the ligand, or some custom index group of residues
surrounding the ligand. Centering on the whole system usually doesn't do
anything useful.
-Justin
Steven
--
========================================
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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