[QE-users] vc-relax on Gelatin molecule
Ying Chunhua
chunhua.ying at wsu.edu
Tue Mar 17 18:59:31 CET 2020
Dear QE Users,
Greetings,
I have been studying QE for half a year, currently I am working on optimizing the crystal structure of gelatin molecule. The initial coordinates was obtained from a protein ‘.pdb’ file of gelatin. I do not know whether it is the best configuration so that I use QE to run the vc-relax.
The problem I have come across is that the ‘forc_conv_thr’ is hard to be achieved, when I plot the history of force(attached), I can see after a certain number of iterations, the total force would vibrate around a certain value(~1e-2) a little bit. Theoretically the total force should be decreasing to 0, I have tried to adjust the input parameters, like ecutwfc(50~150), mixing_beta(0.1 ~ 0.7), bfgs to damp, but not effective. Please give any suggestions on what should I do?
Thanks a lot and Best regards.
Chunhua
The input can be seen below:
&CONTROL
calculation = "vc-relax"
forc_conv_thr = 1.00000e-06
etot_conv_thr = 1.00000e-04
max_seconds = 28800
outdir='./outdir'
pseudo_dir = "/home/chunhua/QuantumEspresso/PAW_precision_pseudos"
restart_mode = "from_scratch"
nstep=100
/
&SYSTEM
degauss = 1.00000e-02
ecutrho = 5.00000e+02
ecutwfc = 1.00000e+02
ibrav = 0
nat = 217
ntyp = 4
occupations = "smearing"
smearing = "gaussian"
/
&ELECTRONS
conv_thr = 1.00000e-04
electron_maxstep = 200
mixing_beta = 1.00000e-01
startingpot = "atomic"
startingwfc = "atomic+random"
/
&IONS
ion_dynamics = "bfgs"
/
&CELL
cell_dofree = "all"
cell_dynamics = "bfgs"
press_conv_thr = 5.00000e-01
/
K_POINTS {gamma}
CELL_PARAMETERS {angstrom}
32.039000 0.000000 0.000000
0.000000 30.039000 0.000000
0.000000 0.000000 50.039000
ATOMIC_SPECIES
O 15.99940 O.pbe-n-kjpaw_psl.1.0.0.UPF
N 14.00674 N.pbe-n-kjpaw_psl.1.0.0.UPF
H 1.00794 H.pbe-kjpaw_psl.1.0.0.UPF
C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
N 7.659071 9.660491 38.488224
H 7.708071 8.734491 38.052224
C 6.804071 9.663491 39.674224
H 6.853071 10.650491 40.137224
C 7.465071 8.662491 40.595224
O 8.658071 8.812491 40.838224
C 5.336071 9.344491 39.352224
H 4.737071 9.431491 40.259224
H 4.958071 10.054491 38.617224
H 5.235071 8.333491 38.958224
H 7.374071 10.281491 37.738224
H 8.609071 9.851491 38.766224
N 6.776071 7.591491 40.987224
H 5.781071 7.627491 41.140224
C 7.457071 6.307491 41.058224
H 8.371071 6.372491 41.651224
H 6.786071 5.570491 41.499224
C 7.783071 5.929491 39.602224
O 7.775071 6.809491 38.735224
N 8.037071 4.655491 39.297224
C 8.114071 4.186491 37.922224
H 8.957071 4.675491 37.431224
C 6.814071 4.500491 37.157224
O 5.889071 3.692491 37.134224
C 8.412071 2.682491 38.034224
H 7.490071 2.098491 38.045224
H 9.056071 2.335491 37.224224
C 9.077071 2.548491 39.407224
H 8.985071 1.541491 39.818224
H 10.130071 2.828491 39.329224
C 8.329071 3.590491 40.237224
H 8.949071 3.928491 41.069224
H 7.395071 3.168491 40.610224
N 6.720071 5.681491 36.545224
H 7.480071 6.349491 36.649224
C 5.608071 6.076491 35.695224
H 4.693071 5.550491 35.973224
C 6.016071 5.766491 34.258224
O 7.163071 5.420491 33.983224
C 5.411071 7.599491 35.816224
H 5.708071 7.920491 36.811224
H 6.083071 8.063491 35.099224
C 4.001071 8.140491 35.553224
H 3.524071 7.632491 34.716224
H 3.394071 7.973491 36.445224
C 4.088071 9.648491 35.257224
H 3.082071 10.070491 35.304224
H 4.690071 10.124491 36.032224
N 4.631071 9.918491 33.908224
H 4.492071 9.204491 33.200224
C 5.273071 11.030491 33.510224
N 5.762071 11.890491 34.403224
H 6.110071 11.454491 35.261224
H 6.192071 12.760491 34.139224
N 5.422071 11.259491 32.203224
H 5.245071 10.476491 31.572224
H 5.846071 12.094491 31.830224
N 5.110071 5.999491 33.312224
H 4.132071 6.031491 33.549224
C 5.520071 6.282491 31.949224
H 6.218071 5.530491 31.578224
H 4.642071 6.304491 31.304224
C 6.180071 7.662491 31.974224
O 5.557071 8.653491 31.577224
N 7.401071 7.755491 32.505224
H 7.804071 6.910491 32.897224
C 8.196071 8.975491 32.522224
H 7.555071 9.791491 32.834224
C 8.669071 9.260491 31.085224
O 8.578071 8.380491 30.229224
C 9.344071 8.853491 33.543224
H 9.373071 7.852491 33.979224
H 10.297071 9.005491 33.035224
C 9.234071 9.874491 34.693224
H 10.177071 9.857491 35.240224
H 9.079071 10.885491 34.326224
C 8.148071 9.550491 35.688224
O 8.194071 8.460491 36.289224
O 7.308071 10.437491 35.978224
N 9.133071 10.482491 30.787224
C 9.503071 10.849491 29.438224
H 8.757071 10.518491 28.713224
C 10.852071 10.214491 29.103224
O 11.894071 10.810491 29.360224
C 9.549071 12.380491 29.442224
H 10.245071 12.777491 28.700224
H 8.548071 12.767491 29.250224
C 9.962071 12.730491 30.872224
H 11.054071 12.696491 30.927224
O 9.597071 13.724491 31.158224
C 9.375071 11.583491 31.706224
H 8.445071 11.901491 32.175224
H 10.114071 11.304491 32.456224
N 10.836071 9.010491 28.531224
H 9.964071 8.501491 28.488224
C 12.025071 8.425491 27.930224
H 12.731071 8.129491 28.703224
H 11.732071 7.531491 27.379224
C 12.601071 9.437491 26.931224
O 11.880071 9.798491 26.000224
N 13.834071 9.936491 27.116224
C 14.391071 10.953491 26.242224
H 13.792071 11.858491 26.354224
C 14.414071 10.499491 24.783224
O 14.896071 9.408491 24.486224
C 15.808071 11.217491 26.760224
H 16.513071 10.539491 26.276224
H 16.116071 12.250491 26.595224
C 15.709071 10.858491 28.242224
H 16.677071 10.593491 28.670224
H 15.270071 11.696491 28.786224
C 14.728071 9.686491 28.237224
H 14.215071 9.654491 29.198224
H 15.264071 8.752491 28.061224
N 13.919071 11.347491 23.883224
H 13.457071 12.185491 24.195224
C 14.074071 11.171491 22.449224
H 14.122071 10.110491 22.197224
C 15.378071 11.860491 22.051224
O 15.777071 12.832491 22.694224
C 12.883071 11.794491 21.717224
H 13.010071 11.668491 20.641224
H 11.959071 11.304491 22.026224
H 12.822071 12.860491 21.941224
N 16.042071 11.368491 21.008224
H 15.698071 10.548491 20.536224
C 17.231071 12.019491 20.481224
H 17.864071 12.351491 21.303224
H 17.786071 11.306491 19.872224
C 16.815071 13.198491 19.596224
O 15.626071 13.341491 19.302224
N 17.769071 14.036491 19.164224
C 17.565071 14.925491 18.032224
H 16.788071 15.649491 18.279224
C 17.180071 14.116491 16.789224
O 17.404071 12.904491 16.745224
C 18.908071 15.635491 17.811224
H 19.474071 15.126491 17.028224
H 18.786071 16.686491 17.542224
C 19.648071 15.464491 19.138224
H 20.731071 15.493491 19.007224
H 19.333071 16.250491 19.826224
C 19.142071 14.108491 19.630224
H 19.221071 14.059491 20.715224
H 19.719071 13.306491 19.167224
N 16.628071 14.801491 15.785224
H 16.423071 15.777491 15.916224
C 16.355071 14.230491 14.471224
H 16.166071 13.159491 14.561224
C 17.620071 14.438491 13.622224
O 18.729071 14.463491 14.161224
C 15.092071 14.890491 13.889224
H 14.335071 14.959491 14.669224
H 15.317071 15.895491 13.531224
C 14.483071 14.072491 12.759224
O 14.898071 14.310491 11.605224
O 13.617071 13.227491 13.064224
N 17.502071 14.628491 12.311224
H 16.573071 14.587491 11.898224
C 18.631071 14.909491 11.442224
H 19.459071 14.234491 11.658224
H 18.317071 14.753491 10.409224
C 19.084071 16.357491 11.615224
O 18.870071 17.178491 10.724224
N 19.702071 16.676491 12.757224
H 19.801071 15.946491 13.453224
C 20.225071 18.006491 13.046224
H 19.349071 18.643491 13.141224
C 21.133071 18.452491 11.879224
O 22.136071 17.791491 11.600224
C 20.921071 18.000491 14.419224
H 20.340071 17.388491 15.111224
H 21.922071 17.572491 14.346224
C 21.008071 19.404491 15.041224
H 21.744071 20.002491 14.504224
H 20.038071 19.895491 14.979224
C 21.398071 19.367491 16.516224
O 21.993071 18.350491 16.933224
O 21.073071 20.356491 17.206224
N 20.779071 19.524491 11.149224
C 21.322071 19.773491 9.823224
H 21.423071 18.836491 9.271224
C 22.694071 20.449491 9.879224
O 22.811071 21.649491 9.631224
C 20.265071 20.634491 9.120224
H 20.680071 21.270491 8.337224
H 19.503071 19.978491 8.697224
C 19.649071 21.432491 10.271224
H 20.326071 22.252491 10.528224
O 18.653071 21.808491 10.007224
C 19.641071 20.395491 11.399224
H 18.718071 19.816491 11.333224
H 19.715071 20.882491 12.373224
N 23.741071 19.684491 10.178224
H 23.569071 18.734491 10.489224
C 25.112071 20.159491 10.042224
H 25.258071 21.021491 10.690224
H 25.789071 19.369491 10.367224
C 25.411071 20.465491 8.564224
O 25.232071 19.564491 7.742224
N 25.815071 21.697491 8.214224
C 26.197071 22.056491 6.858224
H 25.568071 21.561491 6.117224
C 27.664071 21.701491 6.593224
O 28.379071 21.388491 7.573224
C 25.992071 23.570491 6.795224
H 26.602071 24.031491 6.017224
H 24.935071 23.782491 6.630224
C 26.398071 24.013491 8.201224
H 27.487071 24.068491 8.248224
H 25.955071 24.968491 8.483224
C 25.919071 22.857491 9.086224
H 24.938071 23.095491 9.498224
H 26.638071 22.683491 9.886224
O 28.065071 21.808491 5.413224
H 9.931071 13.896491 32.066224
H 18.333071 22.323491 10.780224
-----------------------------------------------------------
Chunhua Ying
Ph.D. Student
School of Mechanical and Materials Engineering
Washington State University
Engineering Laboratory Building, 105
900 NE College Ave, Pullman, WA 99164
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