[gmx-users] Trajectory

[Mark Abraham]

On 31/01/2012 1:07 AM, 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
>
>
>          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?

If ligand A and B start near each other, and each moves and binds to the 
protein but travelling in the opposite direction from the other ligand, 
what would you like to see? This kind of simulation is not like iron 
filings and a magnet :-)

Mark
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