[gmx-users] Trajectory

[Justin A. Lemkul]

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

Is this unusual?  It sounds like the molecules diffuse around until they bind to 
the protein.  You're centering on the protein and then fitting its translation 
and rotation; everything else will be processed relative to those criteria.

-Justin

-- 
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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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