Do I have to rerun the .xtc file obtained after using GPU acceleration?

User discussions
,
1

GROMACS version: 2022.3
GROMACS modification: No
I am a beginner. Do I have to rerun the .xtc file obtained after using GPU acceleration? If necessary, what are the parameters of rerun?
（To add: After MD I also need to use the .xtc file to do the MMPBSA calculation.）
Thank you so much！

2

I don’t understand. Do you mean doing gmx mdrun -rerun? What makes you think you might need that?

3

Thanks for your reply.

Yes, I am not sure whether I need to set the energygrps parameter and do gmx mdrun -rerun in CPU after a GPU-accelerated MD, because the energygrps parameter cannot be set using GPU acceleration.

Especially if I also need to use the obtained .xtc file for MMPBSA calculations.

4

Hope I made it clear.

5

Ok I am starting to understand. If you need the energies for specific groups (such as a protein) then you might need to do mdrun -rerun if the GPU calculations can’t decompose that. The MMPBSA is something I have no direct experience of so I am of little help there.

6

Thank you! It is very helpful to me.