[gmx-users] energy minimization of a box containing two Na+ ions and water does not converge

Ozge Engin ozge.engin at gmail.com
Fri Mar 26 12:39:34 CET 2010

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


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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