[gmx-users] Jumping protein

[Justin A. Lemkul]

Steven Neumann wrote:
> Dear Gromacs Users,
>  
> I run md simulation of protein in water obtaining trajectory. Because in 
> VMD my protein was jumping plus I had some part of my protein shaded in 
> some frames I could not catch one place to create a movie I used:
>  
> 
> trjconv -f md.trr -s md.tpr -pbc nojump -o mdnojump.xtc
> 
>  
> 
> trjconv -f mdnojump.xtc -s md.tpr -center -o mdfinal.xtc
> 
>  
> 
> Now, I have still the same problem - it jumps on my screen but not as 
> much as previously. Can you suggest what can I do to find one place in 
> order to make a movie observing conformational changes?
> 

A more complete workflow is described here:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

>  
> 
> Steven
> 

-- 
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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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