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When I minimise my system , it converges in 14 steps saying the common error that there are overlaps in the structure. I have checked several times and could not find any error in my structure. I did the energy minimisation step in MOE , which converged in several steps and showing less energy . This suggested that the system is free of any overlap due to this . I took the same system and ran in gromacs . But still it showed the same error and the potential energy is too high 1.988 *10^19. What should i do
Could you share a visualization of the structure, the commands you used to set it up and copy-paste the output from the commands (notes, warnings, errors, etc)?
gmx grompp -f em.mdp -c 1newbox.gro -p topol.top -o em.tpr -maxwarn 3
Command line:
gmx mdrun -v -deffnm em
Back Off! I just backed up em.log to ./#em.log.1#
Compiled SIMD: SSE4.1, but for this host/run AVX2_256 might be better (see
log).
Reading file em.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
Back Off! I just backed up em.trr to ./#em.trr.1#
Back Off! I just backed up em.edr to ./#em.edr.1#
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.96433e+19 Fmax= inf, atom= 1251
Step= 14, Dmax= 1.2e-06 nm, Epot= 1.96433e+19 Fmax= inf, atom= 1251
Energy minimization has stopped because the force on at least one atom is not
finite. This usually means atoms are overlapping. Modify the input
coordinates to remove atom overlap or use soft-core potentials with the free
energy code to avoid infinite forces.
You could also be lucky that switching to double precision is sufficient to
obtain finite forces.
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.1#
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 1.9643316e+19
Maximum force = inf on atom 1251
Norm of force = inf
You can see my ligand in which is highlighted in the second picture
Is atom 1251 part of the ligand? Would you be able to shift the position of the ligand to see if that helps lower the energy? (the error could be due to atoms being too close even if they don’t overlap)
The issue got resolved , actually there were two atoms of the ligands that were not matching with the topology.top file . So I corrected that to some extent, by checking the coordinates of the same . When I did that , it was again showing that one atom of the ligand is still not matching with topology file . But this time in energy minimisation step , the system converged and the potential energy was way lesser . I further went on to add my solvent , ions and again energy minimised it , and the system again converged correctly . Thank you for the responses and help .