Re: [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 <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> wrote:



    Steven Neumann wrote:



        On Mon, Jan 30, 2012 at 12:16 PM, Mark Abraham
        <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
        <mailto:mark.abra...@anu.edu.au
        <mailto:mark.abra...@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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