GROMACS version:
GROMACS modification: Yes/No
Here post your question
com.top (22.4 KB)
Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
Back Off! I just backed up em1.trr to ./#em1.trr.3#
Back Off! I just backed up em1.edr to ./#em1.edr.3#
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.05915e+34 Fmax= 7.12759e+07, atom= 7991
Is it because of structural problems that it cannot be operated when energy is minimized?
I would think that it’s due to atoms being too close to each other or a bond that is too long. A good start would be to have a look at atom 7991, all atoms in the same residue as atom 7991 and all atoms within 0.4 nm (0.6 if running a coarse-grained simulation) of atom 7991.
I’d suggest opening the coordinate file (.gro) in, e.g., VMD. And use the representation options (Graphics → Represenations...) to show only the atoms you are interested in, e.g.
same residue as within 4 of index 7990.
This will show all residues with at least one atom within 0.4 nm of atom 7991 (index 7990 in VMD). Then see if all bonds you expect are correctly represented and if there are any atoms in close vicinity. You may want to show the atoms as VdW spheres to make that slightly easier.
No, that is your residue 7991, containing atoms 28077, 28078 and 28079.
That sounds very strange. Do you know if the problem is with VMD or with your gro files?
You’ll probably want some kind of visualization software, so if VMD doesn’t work for you, try another one. Most of them would be able to do similar visualizations, but you’d probably have to check their documentation.
Now that I’ve successfully opened it, where exactly should I find that atom?
I don’t know where your atoms are located. Did you follow my advice above?
Yes, I followed your advice, but I didn’t look for where the atoms were
Could you please elaborate on that more?