<span class="Apple-style-span" style="border-collapse: collapse; "><div>Hello All,</div><div><br></div><div>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.</div>
<div>1. Should the implicit solvent conditions be enabled when I run the energy minimization? </div><div>2. What minimum potential energy should I expect (i know that when explicit water is present, the energy often reaches -10E5 or -10E6)</div>
<div>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. </div><div><br></div><div>Below are 2 example runs I did with implicit_solvent = no</div>
<div>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.</div>
<div><br></div><div><div>emtol = 1000</div><div>emstep = 0.1</div><div>Steepest Descents converged to Fmax < 1000 in 29 steps</div><div>Potential Energy = -4.9613008e+003</div><div>
Maximum force = 6.4596338e+002 on atom 235</div><div>Norm of force = 1.0625026e+002</div><div><br></div><div><div>emtol = 1000</div><div>emstep = 0.01</div></div></div><div><div>
Steepest Descents converged to machine precision in 25 steps,</div><div>but did not reach the requested Fmax < 1000.</div><div>Potential Energy = -3.9642480e+003</div><div>Maximum force = 5.1200122e+003 on atom 416</div>
<div>Norm of force = 3.6602789e+002</div></div><div><br></div><div>Any advice is greatly appreciated. Much thanks!</div><div>- Grace</div></span>