How to solve :2 particles communicated to PME rank 1 are more than 2/3 times the cut-off out?

User discussions
22

Did you used the gro files that provides from ATB server? can you also share the topology file where you inserted all these itp.
zip all the files and upload it in some file-sharing website (or gdrive) and share the link here.

23

For example: You need to use the optimised geometry in the CCl4 topology:

25

I have used original geometry all-atom pdb file of polymer downloaded from ATB and then converted it into gro using pdb2gmx command in gromacs. I will try with the optimised geometry also.
I am attaching the zip file link:

Thanks in advance

26

You should use optimised geometry , it will work!

27

Thank you for your assistance. May I ask one more question? There are two optimized PDB files in ATB: allatom_optimized_geometry and unitedatom_optimized_geometry. Which geometry should I utilize ?

28

all atom would be better.

29

Thank you. I will try this

30

Dear @scinikhil,

Thank you for your assistance. I have successfully equilibrated the system using NPT conditions and have now begun running the MD simulation. However, I now intend to model a water-chloroform interface with some polymer chains. How can I calculate the number of atoms and the size of the simulation box by knowing the density for the MD simulation? Your guidance in resolving this issue would be greatly appreciated. Additionally, could you provide some references for modeling a simulation box?

Thank you once again.