[gmx-users] xtc files

mihammad roos mohammad.roos0325 at yahoo.com
Mon Dec 7 13:17:58 CET 2015

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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