Hi all, I have been trying to calculate the PMF of two NA+ ions in explicit bulk water. First, I tried to calculate the mean force between the two ions at a distance of 0.48 nm, which is big enough than the diameter of the ions. I first energy minimized the system with the script below, but it did not converge. After that, I removed one of the ions, and tried again, it did not work again.
I am using ffG43a1 ff, and checked whether I used the correct naming for the ion: Everything seems to be OK. I could not attach the initial coordinate file due to the limited size. If you want I can also sent it to you as well. *Script: * title = Minimization cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 30000 nstlist = 10 ns_type = grid rlist = 1.0 vdwtype = cut-off coulombtype = PME rcoulomb = 1.0 rvdw = 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.01 *Output*: Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax < 100. Potential Energy = -1.0409969e+05 Maximum force = 9.6685031e+04 on atom 294 Norm of force = 1.4924829e+03 What may be the problem? Best Regards -- Ozge Engin ★☆
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