On 8/11/2011 3:17 AM, Steven Neumann wrote:
On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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
Thank you guys but...
I am trying and it does not work... my ligand is jumping like an idiot
outside the box changing its position even two dimensions of box in
one frame.
I have no idea what you mean by this.
I removed -ur compact from the first line and I tried centering on
ligand or protein (centering group: LIG or Protein, output: SYSTEM).
No results...
My ligand at the begining of the simualtion is not within the protein.
Please, help :(((( I tried this workflow with many ligands and same
protein - it worked! Now it does not...
Sure. So far you've given us no understanding of what your ligand is
doing during the simulation. If you don't know either, go and look at
it. Then go and look at the trajectory from each stage of your work flow
and see what it looks like and how things are changing. Then when
something looks wrong you have a single step you can trouble shoot...
maybe the operation is not sensible, maybe the way you did it is wrong,
maybe the code is wrong.
You cannot expect to transfer work flows from another simulation without
considering what is happening in this one. Scenarios where your ligand
is diffusing away from your protein and reassociating to another side
require different work flows from one where the ligand stays nearby a
binding pocket. In the latter, you should probably use -pbc cluster in
step 2, though some of the time it won't matter. In the former, using
-nojump to allow diffusion out of the box, and then step 6 to put
everything back in the box doesn't make sense. Just doing operations and
selecting groups without considering the nature of the operation will
get a garbage result. There's a good reason mdrun doesn't attempt to
second-guess how you would like all of this done!
Mark
Here is my workflow:
1.First make your molecules whole if you want them whole.
trjconv -f md.trr -s md.tpr -pbc whole -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
(system)
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 (tried centering on
LIG or PROTEIN)
trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -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
With point three, the issue is that trjconv
<http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv>
removes the jumps from the first frame using the reference structure
provided with |-s|. If the reference structure (run input file) is not
clustered/whole, |trjconv -|pbc|nojump|will undo steps 1 and
Steven
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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