[gmx-users] Trajectory

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Mon, Jan 30, 2012 at 1:46 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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
>         <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
> 
> Sorry, I did not clarify it properly. What is unusual is that
> my ligands (until they bind) jump to its periodic images. It is a speed 
> light diffusion :) Any suggestions?
>  

Nope.  As I said, you fitted everything on the protein (which is sensible). 
Everything else is manipulated accordingly.  Perhaps it's a bit inconvenient to 
watch, but there's no real way to avoid periodic jumps of every molecule 
simultaneously, you need a reference position, which for you is the protein.

-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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