Discrete "Coulp.-recip" values for different conformations of the same system

User discussions
1

GROMACS version: 2023.2
GROMACS modification: No
Hello everyone,

I calculated the average energy terms for XG in water across 25 different conformations. All systems are identical, sharing the same water molecules; the only difference is the conformation of XG. Specifically, I analyzed the “Coulp.-recip” term, as shown below. The x‑axis values, such as “60000–65000,” represent the conformation names, while the y‑axis values correspond to the difference between each system and the lowest value.

image
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However, the “Coulp.-recip” values appear discrete. It should be random. In my MDP setup, the coulombtype in the .mdp file was set to PME. I also tried adjusting the parameters:

fourierspacing = 0.08  
pme_order = 6  
ewald_rtol = 1e-6

…but the values remain discrete.

Do you have any suggestions or insights on this? Thank you very much!

2

This is very strange. Is the unit completely filled with a uniform water density? Are the box sizes the same?

3

Yes, the box sizes are totally the same. The water was filled automatically by Gromacs program.

4

One thing to check: PME tuning could explain this, if it is active. The split between Coul.-recip and Coul SR depends on the Ewald splitting parameter. mdrun -notunepme disactivates tuning.

5

Thanks a lot. I will try.

6

Thank you very much for this suggestion！Disabling PME tuning with -notunepme resolves the issue. You were absolutely right！This was very helpful！

7

Note that this is not really an issue, as the decomposition of the Coulomb energy is artificial. You should only look a the total Coulomb energy.

8

Yeah. Thanks a lot for the clarification! It makes sense.