GROMACS version: 2022.3
GROMACS modification: No
I’ve been building different membrane protein systems with CHARMM-GUI to simulate in gromacs and got stuck troubleshooting an instability. From the initial run, these are the different energy terms in the .edr file:
1 Bond 2 U-B 3 Proper-Dih. 4 Improper-Dih.
5 CMAP-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR)
9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Kinetic-En.
13 Total-Energy 14 Conserved-En. 15 Temperature 16 Pressure
17 Constr.-rmsd 18 Box-X 19 Box-Y 20 Box-Z
21 Volume 22 Density 23 pV 24 Enthalpy
25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX
29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY
33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ
37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX
41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX
45 Box-Vel-YY 46 Box-Vel-ZZ 47 T-SOLU 48 T-MEMB
49 T-SOLV
Digging through them the blowup is happening with a positive spike in kinetic energy/temperature of the solvent and a negative spike in pressure.
However, when I try saving trajectories of different components (solvent, protein, membrane) and using mdrun -rerun to compute these terms on the subsystems most of the energy terms are not calculated and I’m left with 9 that didn’t have any anomalies in the original simulation.
1 LJ-(SR) 2 Coulomb-(SR) 3 Coul.-recip. 4 Potential
5 Box-X 6 Box-Y 7 Box-Z 8 Volume
9 Density
I’ve been trying to figure out why the energy terms are limited for reruns, which occurs even if I rerun the full simulation with the same .tpr and .edr files from the original output provided.
If anyone has any ideas, suggestions, or clarifications please let me know!