[gmx-users] Trajectory

[Steven Neumann]

On Mon, Jan 30, 2012 at 12:16 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 30/01/2012 8:43 PM, Steven Neumann wrote:
>
> Dear Gmx Users,
>
> I run the simulation of protein with 10 ligands (200 ns). In total I
> should have total of 4000 frames as I set up:
>
> nsteps = 100000000
>
> dt = 0.002
>
> nstxout = 25000
>
>
> ... iff the simulation completed successfully.
>
>
>  I used trjconv -f md.trr -o mdnojump.xtc -pbc nojump
>
> The trajectory which I read in VMD has 3008 frames and my ligands
> completely disappear after 8 frame (They are not in PBC windows which I
> checked in Graphics -> Graphical Representation -> Periodic)
>
>
> Your choice of trjconv workflow demands that the protein be allowed to
> diffuse away. What VMD makes of that is not really of consequence to
> discuss here. Perhaps you can design a better trjconv workflow, as here
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
>
 Thank you. I managed to fix it using:

trjconv -f md.trr -o md1000.xtc -skip 4  (1000 frames instead of 4000)

Then accoring to the workflow (PBC) I used:


trjconv -f md1000.xtc -s md.tpr -pbc mol -o mdmol.xtc

trjconv -f mdmol.xtc -s md.tpr -center -o mdCENTER.xtc  (Center on a
protein, output - System)


trjconv -f mdCENTER.xtc -s md.tpr -fit rot+trans -o mdFit.xtc (Protein,
output - System)



However, all ligands jump rapidly

 around the protein till the time they bind to the protein surface (and the
begining they were randomly placed around the protein) one by one. At the
end when all of them stacked on my protein everything is ok. Will you
suggest something?



thank you,



Steven





>
>  Can you please advise? I think I have to many frames in my trajectory,
> how can I reduce it in trjconv?
>
>
> trjconv -h
>
> Mark
>
>  Thank you,
>
>
>
> Steven
>
>
>
>
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