[gmx-users] energy minimization of a box containing two Na+ ions and water does not converge
ozge.engin at gmail.com
Fri Mar 26 12:39:34 CET 2010
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
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.
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?
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users