GROMACS version:2021.3
GROMACS modification: No
I build a mem_protein system, in this system, I use graphene act as mem. But when I try to run the em progress,
Step= 0, Dmax= 1.0e-02 nm, Epot= 4.66041e+34 Fmax= 7.66920e+05, atom= 1036
Step= 14, Dmax= 1.2e-06 nm, Epot= 4.66041e+34 Fmax= 7.66918e+05, atom= 1036
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 4.6604085e+34
Maximum force = 7.6691950e+05 on atom 1036
Norm of force = 1.6602782e+04
then, I check the atom 1036, I don’t find any exception. What should I do? Thank you.
minim.mdp (1.0 KB)
md.mdp (1.3 KB)
topol.top (373.6 KB)
ions.mdp (1.2 KB)
mdout.mdp (10.2 KB)
You’ve probably got a problem in your starting geometry (e.g. two atoms very close together). If you read your .gro file into VMD and look at atom 1036 can you see what’s wrong?
Thank you for your answer. I checked my starting geometry. The atom 1036 is the part of my protein, and I downloaded if from OPM website.
red is 1036 and green is 1035
In another simulation, I uploaded the protein to CHARMM-GUI, and I build a mem_protein system. There is nothing wrong happened.
Zooming in on that atom is not particularly useful - what is around that atom, that is, what are its interactions? Is the geometry of the constituent residue reasonable?
Thank you very much. In this case, what should I do to check atom 1036’s interactions and the constituent residue reasonable?
It’s a matter of visual inspection. Look around. Anything that has a potential energy of 1034 should have an extremely close contact (nearly superimposed atoms) or some totally distorted geometry.
If you can’t identify it, upload your coordinate file so we can have a look.
Hi, jalemkul. Because of the limits of the upload. I modified the file extension from *gro to *mdp. You need to change it to *gro. The explain.mdp contains the meaning of my files. In the meanwhile, I found the edge of bilayer graphene (em.gro) is strange. Thank you very much.
mem_protein.mdp (120.7 KB)
mem_protein_whole.mdp (627.8 KB)
em.mdp (623.0 KB)
expalin.mdp (608 Bytes)
mem_protein_box.mdp (120.6 KB)
whole_ions.mdp (623.0 KB)
Atom 1036 resides in residue Tyr1021, which is the C-terminal residue in the chain. The specific carbonyl group that has the problem has no terminus to it, it’s a dangling C=O group. You need to build an appropriate carboxy terminus onto this polypeptide chain, it’s chemically incomplete. This is causing unphysical outcomes.
Thank you very much. You mean this structure has no terminus in atom 1036, which indicates the structure is chemically incomplete. I downloaded this structure from OPM website, then I picked part of it in my structure. What should I do to build an appropriate carboxy terminus onto this polypeptide chain. Thank you again!
Choose a valid terminus when prompted by pdb2gmx. The only way you could have generated a topology for this system would have been to have done this and chosen “None” as the terminus (and perhaps also allowed for missing atoms, which is problematic).
Yeah, you are right. When I use pdb2gmx to get top file. There is an error (missing atoms). So I used CHARMM-GUI to get top file. Anyway, I will try your method. Thank you very much.