[gmx-users] Protein Moving Out of Box in ED

Xavier Periole X.Periole at rug.nl
Tue Jan 22 10:21:59 CET 2008

On Tue, 22 Jan 2008 08:39:04 +0000 (GMT)
  Anirban Ghosh <anirbanz83 at yahoo.co.in> wrote:
> Hi Friends,
> I am simulating a 463 aa protein in water only along the 1st Eigen Vector 
>i.e. I am trying to do Essential Dynamics along First Principle Component. I 
>have used the make_edi command to generate a .edi file and then using it to 
>run the mdrun. But my problem is that every time after a simulation of 5 nano 
>second, I am finding that the pretein is coming out ofthe water box, 
>partially. I am using VMD to view the dynamics after the simulation is 
>complete. Is it a problem with GROMACS or VMD or is it that since I am using 
>Periodic Boundary Condition, the portion of the protein which is looking to 
>be outside the box, is actually inside another adjacent box, partally? Is 
>there any way to rectify this or am I doing the correct thing? Please 
>suggest. Any suggestion is welcome. Thanks a lot.

This is due to the use of periodic boundary condition.

Actually the whole protein should go in and out of one side to the
other of the box! You might have used the -pbc inbox option in trjconv?

To fix it you can either:
1: trjconv -f input.xtc -o output.xtc -pbc nojump
this will remove the jumps of in/out of hte box and show the protein
diffusing freely in space.
2: trjconv -f input.xtc -o output.xtc -fit rot+trans -n index.ndx -o ref.gro
this will allow you to remove the translation and rotation of the protein
and place it on a reference fame using a set of atoms that you can
define in index.ndx. If the ref.gro is a conformation at the center of
the box ... then you got your trajectory with the protein at the center.


> Cheers,
>  Anirban Ghosh
>  M.Tech Bioinformatics
>  University of Hyderabad
> Project Trainee
> Centre For DNA Fingerprinting & Diagnostics (CDFD)
> Hyderabad
> India
> ---------------------------------
> Why delete messages? Unlimited storage is just a click away.

XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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