Hi,
An energy minimization step I converged to machine precision with the following values:
Potential Energy = -5.0373220e+06
Maximum force = 1.1988365e+03 on atom 6641
Norm of force = 6.7971182e+00
The tolerance was accidentally set to 100. The system is a protein complex. The total number of atoms is 72362, with 20,720 water molecules (62,160 atoms).
Is the maximum force the system reached considered reasonable for my system?
Thanks.
In your case, the maximum force was 1.1988365e+03 kJ/mol/nm, which is much higher than the ideal range. Further minimization may be necessary.
Hi, my rule of thumb is that the tolerance value should be equal to or less than the number of residues in the system. It is fairly crude but never disappointed me.
You can manually inspect atom 6641 (its residues; open gro file in chimera) and see why it is not getting minimized. There may be some elemental conflict that is preventing it from moving/minimizing. If it is, then your next step will fail as well. So, better fix it here.
Further minimization is recommended but also depends on the objective of running MD. For instance, NMA required a properly minimized system, while simple protein-protein interaction and other dynamic analyses can work without thorough minimization.
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