[gmx-users] Why GROMACS is generating so many output trajectory files?

[Swapnil Wagle]

Hi..!

I am having a system with 450 Protein atoms and ~9000 water atoms. When I am trying to do the energy minimization step, it gives me hundreds of trajectory files (all .pdb with names like Step**_**.pdb). I am using gromos 53a6 force field with TIP4P water model. The error message also says something like (one atom moved too far during the domain decomposition steps) which is not quite visible when I load the initial structure in VMD. The simulation completes sometimes but sometimes it also stops in the middle. Can you suggest me what can possibly be wrong, or any suggestion about how to remove this error?

Regards,
Swapnil Wagle
Department of Theory and Bio Systems
Max Planck Institute for Colloids and Interfaces
Potsdam-Golm, Germany D-14424
Tel.: +49-331 567-9607
Mail: Swapnil.Wagle at mpikg.mpg.de<mailto:Swapnil.Wagle at mpikg.mpg.de>