Minimization issue

User discussions
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1

hello
i am a new user. I am doing pure simulation of phospholipids , membrane contains 100 dop molecules and 2000 water molecules so each layer contains 50 dop molecules and 1000 water molecules i face this issue how to fix this problem . i have also attached my minimization.mdp file for brief explanation. When i see my structure completly broken
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)

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 1.3146015e+32
Maximum force = 1.3916486e+11 on atom 5791
Norm of force = 6.6033586e+09
Finished mdrun on rank 0 Mon Jul 29 16:36:33 2024

minim.mdp (983 Bytes)

2

I notice you have define = -DPOSRES in the mdp which is calling position restraints and likely interfering with the minimization. Could you try removing that from the mdp?

3

The .mdp looks fine to me. How did you build the system? That’s a very large potential energy/force, likely coming from clashes.

4

yes i have already deleted but still the same errors

5

Then as @obZehn mentioned, are you able to find any clashes in the system? When you ran the minimization, it should output which atoms it was trying to perturb, could you check which atoms it got stuck on the visualize the system to see what might be causing any clashes?

Since it’s a membrane simulation, it might be helpful to check whether some of these suggestions apply