I started minimizing a solvated protein-ligand structure with emtol = 1000 then I tried to reduce the tolerance until I reached 100 and it achieved a maximum force of 99.9 with a potential energy of -927980 but when I tried to make emtol = 50 it said that it could not reach this value and saved coordinates with max force = 321 and a potential energy = -929472
so which is better a low max force or a low potential energy?
"There are two very important factors to evaluate to determine if EM was successful. The first is the potential energy (printed at the end of the EM process, even without -v). Epot should be negative, and (for a simple protein in water) on the order of 10^5-10^6, depending on the system size and number of water molecules. The second important feature is the maximum force, Fmax, the target for which was set in minim.mdp - "emtol = 1000.0" - indicating a target Fmax of no greater than 1000 kJ mol-1 nm-1. It is possible to arrive at a reasonable Epot with Fmax > emtol. If this happens, your system may not be stable enough for simulation. Evaluate why it may be happening, and perhaps change your minimization parameters (integrator, emstep, etc)."
That what was mentioned in official Gromacs tutorials at http://www.mdtutorials.com/gmx/lysozyme/05_EM.html
I hope that might be of help!
Marwa Abd El Kader Zaater Thank you. in my case the difference between the two runs for potential energy is just 2000. so i think the larger potential with a low fmax structure is better, right?
Dear Ibrahim M. Ibrahim , I think yes the first case you mentioned is better with lower Fmax, but is the the PE value ended in e^5 or e^6?
Marwa Abd El Kader Zaater both are e^5.
Martin Klvana to minimize the potential energy. however, in gromacs only (as far as i know), it produces the fmax also. so i was asking if fmax is large with a low PE better than the case when fmax is low with a slightly high PE.
Ibrahim M. Ibrahim -- I use energy minimization to remove intermolecular steric clashes in protein-ligand complexes obtained by high-clash tolerance docking and to optimize local interactions (with induced-fit docking-like results). The larger the clash, the higher the force. Total potential energy is not that much relevant. That said, to overcome larger energy barriers, a short molecular dynamics (MD) simulation at 5 K is more effective. So if you want to run MD simulation, and if there are no severe steric clashes, no energy minimization is needed at all, provided that you equilibrate the system carefully, starting at low temperature and with strong bath coupling.
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