System is exploding?

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1

GROMACS version:2021
GROMACS modification: Yes/No
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Hello,

I have been trying to run a protein-ligand complex simulation following the Gromacs tutorial and I keep getting this error when I try to perform the energy minimization step:

Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 32 atoms. The longest distance involved in such interactions is
8.371 nm which is above half the box length. Either you have excessively large
distances between atoms in bonded interactions or your system is exploding.

I tried troubleshooting this issue by simulating the protein itself as per suggestion from the Gromacs manual and the protein is clearly stable, so maybe the ligand is the issue in Gromacs? The ligand I am using it 5-methyluridine and I have checked its structure several times. Will someone please guide me through how I can solve this error? I have retried this simulation many times now…

2

Hi @Syeda ,
Can you check that the non-bonded cutoff is smaller than half of the box length. Besides, you can increase your box size and try the minimization.
Regards
Anirban

3

What happens when you simulate the ligand alone? Is that simulation stable? What is the source of the parameters for the ligand, and were they properly validated? What is in your .mdp file?

4

Hello @Anirban12 , @jalemkul ,
I have tried increasing the box size and it still gave me the same error.
I am not sure how to simulate the ligand alone. The ligand parameters are the ones that were generated during the topology step. I have tried using the parameters of the ligand from the CHARMM GUI website to see if that would make a difference, but I was unable to complete the next step because the program said it “could not overwrite the file because there is no space”. My ions.mdp file and em.mdp file are the exact same ones from the protein/ligand tutorial. I have tried using a smaller ligand, methanol, to see if there is some fault in my ligand preparation, and that energy minimization converged. I am not sure if it is not converging for 5-methyluridine because it is too big or some other property.