I am trying to minimize energy in my protein, but xmgrace gave me a slightly negative curve. I tried to decrease Emtol to 100 but the effect was almost the same. The simulation is carried out in a water environment. I also can’t do nvt equilibration now because it stops on 0 step.Is it possible that it is caused by hydrophobic character of fab domain of my antibody? I need help, please.
There are two very important factors to evaluate if energy minimization was successful. The first is the potential energy (printed at the end of the EM process). The second important feature is the maximum force, Fmax, the target for which was set in minim.mdp - “emtol = 100” - indicating a target Fmax of no greater than 100 kJ/(mol nm). 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).
Would you please share the lines printed at the end of the EM process?
thanks for answer
Unfortunately I closed terminal window, so
it is em.log and minim.mdp file for minimization with emtol=100
em.log (2.7 MB)
minim.mdp (1.0 KB)
Steepest Descents converged to Fmax < 100 in 7687 steps
Potential Energy = -3.3881330e+06
Maximum force = 9.0538429e+01 on atom 5682
Norm of force = 2.9952054e+00
Finished mdrun on rank 0 Sun Nov 19 22:51:40 2023
Firstly, please avoid posting the same question twice (see Minimization curve ). Justin has replied there. In that thread, please provide the output and logs from the crashing nvt equilibration. That is where the problem occurs. The energy minimization looks fine.