modified on 18 February 2011 at 13:50 ••• 7,544 views

QMMM NEB example with path limits

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Here is an example of QM/MM NEB calculations, which involves generation of the initial guess for the pathway based on restart files for starting (cloh_rs.rst) and ending (cloh_ps.rst) point. The reference restart file (cloh_neb.rst) is simply a copy of starting (cloh_rs.rst) restart file. As always all the restart and topology (cloh.top) files have to reside in the top level directory. It is very important to explicitly set permanent and scratch directory to be distinct from top level calculation directory.

This particular system consists of Cl- and OH radical species in aqueous solution. The reaction pathway will only involve coordinates of Cl- and OH, which constitutes the QM region. A total of 10 beads will be used, using 5 NEB refinement steps with initial step size of 1.0. The solvent part of the system will be always optimized with respect to current bead configuration, involving in this case 1000 steepest descent iterations (see region, maxiter directives). During solvent optimization, QM region will be represented by point ESP charges (see espfit directive). The entire example directory including output file can be downloaded here.


memory total 1500 Mb

start cloh

permanent_dir ./perm
scratch_dir   ./data
charge -1

basis "ao basis"
 * library "6-31+G*"
end

dft
mult 2
XC b3lyp
iterations 5000
end

md
 system cloh_neb
 cutoff 1.0
end

qmmm
bqzone 10.0
region  solvent
maxiter 1000
ncycles 1
density espfit
end

set qmmm:neb_path_limits cloh_rs.rst cloh_ps.rst

set neb:nbeads 10
set neb:stepsize 1.0
set neb:steps 5

task qmmm dft neb