[gmx-users] PBC - Protein - ligand

[Tsjerk Wassenaar]

Hi Steven,

Don't use -ur compact in the first step and see if that solves the problem.

Oh, and be sure that the thing is not just diffusing. There was a
thread lately where a diffusing ligand drove someone mad trying to
remove the 'jumps'.

Cheers,

Tsjerk

On Mon, Nov 7, 2011 at 3:08 PM, Steven Neumann <s.neumann08 at gmail.com> 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?
>
>
>
> Steven
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands