[gmx-users] Trajectory

[Steven Neumann]

On Mon, Jan 30, 2012 at 1:46 PM, Justin A. Lemkul <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 <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?


> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
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