Hello All, I am doing energy minimization on a protein crystal structure to relax it. Afterwards, I plan to run md simulation with implicit solvent. I am new at this and have many questions. 1. Should the implicit solvent conditions be enabled when I run the energy minimization? 2. What minimum potential energy should I expect (i know that when explicit water is present, the energy often reaches -10E5 or -10E6) 3. What kind of emtol is appropriate? Is it better to set it high so that the system converges, or is it okay if machine precision is reached.
Below are 2 example runs I did with implicit_solvent = no When I decreased the step size, the system did not converge anymore. I was wondering if this was due to chance, precision issues (I am using single precision), or perhaps the emstep = 0.1 was reaching a nearby minimum and 0.01 was reaching the local minimum. Note, maximum force gets rather large when convergence is to machine precision. emtol = 1000 emstep = 0.1 Steepest Descents converged to Fmax < 1000 in 29 steps Potential Energy = -4.9613008e+003 Maximum force = 6.4596338e+002 on atom 235 Norm of force = 1.0625026e+002 emtol = 1000 emstep = 0.01 Steepest Descents converged to machine precision in 25 steps, but did not reach the requested Fmax < 1000. Potential Energy = -3.9642480e+003 Maximum force = 5.1200122e+003 on atom 416 Norm of force = 3.6602789e+002 Any advice is greatly appreciated. Much thanks! - Grace
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