Hi, I'm the beginner in simulation MD, I have problem in energy minimization, may you guys help me?

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Here post your question 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.

Hi Tresia,

Could you please elaborate on your problem. From your message it appears that there is no specific problem with your energy minimization process.

hi, i don’t know how to explain this problem, but according to my Lecture He say that it is have a error
step 18: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 63: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

i think this error in step 18 and 63

can you help me to fix that?
someone just recommend to do this " You may go for the two-step minimization; steepest descents followed by conjugate gradient minimization, and then check the energies. It may fix your problem." But still can not fix this problem :')

You need to tell us more about what you’re doing. What is in your system? Is there anything non-standard (like a ligand) that you have parametrized yourself? What was the actual output from mdrun when you did minimization, that is, what Fmax and Epot were achieved (please copy that section directly from the .log file and provide it).

this is the Fmax and Epot from em.log
Tolerance (Fmax) = 1.00000e+03
Steepest Descents converged to machine precision in 866 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -2.8375678e+05
Maximum force = 2.2208766e+04 on atom 5166
Norm of force = 2.0604174e+02

Start by looking at atom 5166 and whatever is around it. Often you can find some kind of bad clash or incorrect geometry. And please answer my previous questions, they are quite important to tracking down what’s going on. We don’t know what you’re doing. You have to tell us, or we can’t help.