wiki:AlanineDipeptide

Alanine dipeptide

Ground state calculation and molecular dynamics simualtion using the PBE exchange-correlation functional.

Pseudopotentials

Input files

ala2.i: unit cell definition and atomic positions (attachment:ala2.i)

# Ala2
set cell 25 0 0  0 25 0  0 0 25
species carbon    C_ONCV_PBE-1.0.xml
species nitrogen  N_ONCV_PBE-1.0.xml
species oxygen    O_ONCV_PBE-1.0.xml
species hydrogen  H_ONCV_PBE-1.0.xml
atom C1 carbon    -6.579400    -3.078900     0.423100
atom C2 carbon    -4.511500    -1.253100    -0.225200
atom H1 hydrogen  -8.413100    -2.443100    -0.377900
atom H2 hydrogen  -6.765500    -3.219500     2.507900
atom H3 hydrogen  -6.120300    -4.970600    -0.359000
atom O1 oxygen    -5.005800     0.613000    -1.495200
atom N1 nitrogen  -2.104100    -1.704800     0.574900
atom C3 carbon     0.000000     0.000000     0.000000
atom H4 hydrogen  -1.779900    -3.342200     1.579200
atom C4 carbon    -0.381900     2.556000     1.339600
atom H5 hydrogen  -2.167500     3.479100     0.756300
atom H6 hydrogen   1.166700     3.891900     0.879600
atom H7 hydrogen  -0.430800     2.277300     3.420300
atom C5 carbon     2.546000    -1.110900     0.778300
atom H8 hydrogen   0.070900     0.285900    -2.081500
atom O2 oxygen     2.640700    -3.138700     1.886300
atom N2 nitrogen   4.721200     0.150600     0.206800
atom C6 carbon     7.208000    -0.783700     0.879500
atom H9 hydrogen   4.620700     1.839000    -0.758500
atom H10 hydrogen  7.139400    -2.611600     1.907100
atom H11 hydrogen  8.167200     0.623300     2.104200
atom H12 hydrogen  8.342700    -1.050000    -0.864300

Ground state calculation

gs.i
Qbox input file for the ground state calculation (attachment:gs.i)
ala2.i
set ecut 60
set xc PBE
set wf_dyn PSDA
set scf_tol 1.e-8
run -atomic_density 0 30 10 
save gs.xml
gs.r
Qbox output file for the ground state calculation (attachment:gs.r)
Ground state energy: <etotal> -93.12947643 </etotal>

Molecular dynamics simulation

Simulation temperature 400 K, total duration 0.1 ps.

md.i
Qbox input file for the molecular dynamics simulation (attachment:md.i)

set nrowmax 64
load gs.xml
set xc PBE
set wf_dyn PSDA
set scf_tol 1.e-6
set atoms_dyn MD
set dt 10
set thermostat BDP
set th_temp 400
randomize_v 600
run 400 5 
save md.xml
md.r
Qbox output file for the molecular dynamics simulation (attachment:md.r)

The Kohn-Sham energy (<etotal>) and the constant of the motion (<econst>) can be plotted using the econste.plt script provided in the util directory: Plot of the Kohn-Sham energy and constant of the motion

Last modified at 2016-10-24T21:15:30Z Last modified on 2016-10-24T21:15:30Z

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