Re: [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  
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 
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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[gmx-users] xtc files

[mihammad roos]

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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Re: [gmx-users] xtc files

[Vitaly V. Chaban]

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 
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.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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