[gmx-users] xtc files

[mihammad roos]

Thank you Vitaly,


 
But my first system (protein solvated in water) is cubic andas I mentioned in the trajectory file resulted after the production MD (xtcfile) the protein jump from one position to another immediately, is it ok?

And I think the attached image of xtc file is not ok. Does thetopology or the coordinate file from amber have problem? Or it could be fromthe commands which I used in gromacs?

 


    On Monday, December 7, 2015 4:17 PM, Vitaly V. Chaban <vvchaban at gmail.com> wrote:
 

 gromacs does not support "spherical" boxes, as well as I do not think this
would have been correct in view of PBC. No PBC will eventually lead to the
spherical cluster representation.





On Mon, Dec 7, 2015 at 10:07 AM, mihammad roos <mohammad.roos0325 at yahoo.com>
wrote:

> Hello everybody,
>
>
>
> I generated the initial structure by amber tools (the systemis consisted
> of a protein with some ions that the whole system is solvated inwater),
> then convert the top and crd files to gromacs topology and gro files(by
> using parmEd), and then run the equilibration and the production MD
> ingromacs. Now I have the trajectory file(.xtc file)( using“gmx trjconv”
> command) after running the production MD but I think thereis something
> wrong, when I load the xtc file in vmd the protein jump from oneposition to
> another position immediately. Actually I put the protein in thecenter when
> generating the system. Is it a trouble?
>
>
> I attached an image of the xtc file resulted from runningthe production MD
> (using gmx mdrun command notusing gmx trjconv command ), I think the bonds
> are not ok, but when loading thextc file resulted from gmx trjconv the
> bonds seems good. I don’t if there is aproblem or not
>
>
> By the way I generated another system with a protein and somelipids around
> it which is solvated in water by amber tools (the box shape is
> spherical),when I convert it to gro and gromacs topology the gro file is ok
> (it isspherical) but after running the production MD when I open the
> trajectory filethe box is cubic and it is very confused. I want the system
> to be spherical.
>
>
>
> Thank you, Mohammad.
>
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