[gmx-users] energy minimization of a box containing two Na+ ions and water does not converge
Justin A. Lemkul
jalemkul at vt.edu
Fri Mar 26 12:44:59 CET 2010
Ozge Engin wrote:
> 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.
Irrelevant. If naming were an issue, grompp would have failed with a fatal error.
> 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
> 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?
Not a clue. What is atom 294? Look at the output - what are the other nearby
atoms that could be causing the excessive force?
> Best Regards
> Ozge Engin
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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