[gmx-users] EM and an error: Water molecule starting at atom 5113 can not be settled.

[Ali Alizadeh]

Dear All users

1- I got an error when i wanted to perform EM,  my emtol = 100 but it
did not converge

 Water molecule starting at atom 5113 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
...

I saw the pdb files and understood what did the happen,
For solving this error, so i want to perform EM with emtol=1000

it converged,  in next step i got em.gro as a input file and perform
another EM with emtol=900

It converged , and i continued to emtol=100

Is my method true?  I do not know my energy profile(i got by this
method)  is correct,

2- Does this parameter affect on my md production? (when i use
emtol=1000 or emtol=100)


-- 
Sincerely

Ali Alizadeh