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Hi, Sir
“I performed a CG simulation of a symmetric bilayer membrane. After the energy minimization step, patches appeared in the membrane, a gap formed between the water molecules and the lipid bilayer, and the energy minimization did not converge to F max<10. I proceeded with the equilibration (NVT) step, but the gap in the lipid bilayer still remains. I have attached my command-line inputs, the output text file, and a picture of the bilayer for reference. Could someone help me resolve these issues?”
Hi, sir
Apologies for the delayed response. I was able to resolve the issues with my inner leaflet symmetric simulation by using semi-isotropic NPT equilibration.
However, during the energy minimization step of my outer leaflet symmetric simulation, I am encountering a LINC error. This error occurs due to the NMC atom in the DPG3 lipid. I have tried increasing the system’s XYZ box dimensions and reducing the percentage of DPG3 lipids to 1%, but neither solution has resolved the issue. When I proceed with the equilibration step also, the same LINC error appears again. This lipid is essential for my simulation, so I cannot proceed without it.
Could you please suggest a solution for this error? I have attached the error text file and the minimization MDP file for your reference.
It’s difficult to say exactly what the problem is. I’m almost certain that it is a bond that is too long or two atoms/beads that are too close to each other. I would suggest taking a closer look at all beads within 0.6 nm of bead (atom) 2474 (highest force at step 0) and all beads in the same residue as 2474.
I’ve already checked in VMD that the NMC atoms (DPG3) are close together, and increasing the box dimensions didn’t resolve the issue. The simulation runs well without this lipid, but I specifically need it for my study.
Currently, I’m running a simulation with position restraints, and I’ll let you know if it works out.
I have one more question: if I manually adjust the positions of the overlapping atoms to increase the distance between them, will it significantly affect the lipid structure?
If the atoms in the lipid are placed too close to each other, or too close to atoms in a neighboring lipid, I would definitely recommend moving them by hand. You can probably see what offset would be needed. Hopefully, you won’t need to move them very far, which means that it shouldn’t affect the structure very much. The input structures are usually rough estimates anyhow.
Hi, sir
When I keep two atoms of the DPG3 lipid at a distance, two other atoms in the same DPG3 lipid display a LINCS error. To troubleshoot, I started running the simulation without including this lipid.
I used the sphingomyelin lipid ITP file from this GitHub link: Martini Force Field Initiative - M3 Lipid Parameters. As suggested in the documentation, I added martini_v3.0.0_ffbonded_v2_openbeta.itp to the topology file.
However, during the minimization step, I encountered an invalid order directive bondtypes error (screenshot attached). I also tried placing the bondtypes section after the angles section, but the same invalid order error persisted.
You can’t have any [ *types ] directive after the first [ moleculetype ]. See Common errors when using GROMACS - GROMACS 2023 documentation for more information. Check your topology files, you’ll probably just have to reorder things and/or move some definitions.
