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**************************************************************************** | |
*************** DALTON2011 - An electronic structure program *************** | |
**************************************************************************** | |
This is output from DALTON Release Dalton2011 (Rev. 0, July 2011) | |
---------------------------------------------------------------------------- | |
NOTE: | |
DALTON is an experimental code for the evaluation of molecular | |
properties using (MC)SCF, DFT, CI, and CC wave functions. |
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import random | |
import pylab as plt | |
npart = 100 | |
nsteps = 10000 | |
dt = 0.001 | |
X = [random.random() for i in range(npart)] | |
Y = [2*(random.random()-0.5) for i in range(npart)] |
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import random | |
import pylab as plt | |
npart = 100 | |
nsteps = 10000 | |
dt = 0.001 | |
X = [random.random() for i in range(npart)] | |
Y = [2*(random.random() - 0.5) for i in range(npart)] | |
dX = [2*(random.random() - 0.5) for i in range(npart)] |
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for i in range(npart) | |
X[i] = X[i] + dt*dX[i] | |
Y[i] = Y[i] + dt*dY[i] |
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if abs(X[i] + dt*dX[i])>1: | |
dX[i] = -dX[i] | |
if abs(Y[i] + dt*dY[i])>1: | |
dY[i] = -dY[i] |
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simulator_ui.py: simulator.ui | |
pyuic4 simulator.ui -o simulator_ui.py | |
clean: | |
rm -f *.pyc |
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simulator_ui.py: simulator.ui | |
pyuic4 simulator.ui -o simulator_ui.py | |
clean: | |
rm -f *.pyc *~ |
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from qm import Gamess | |
from util import loadOBMoleculeFromFile | |
mol = loadOBMoleculeFromFile('myfile.xyz') | |
method = Gamess(mol) | |
E = method.getEnergy() | |
print E |
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def getAminoAcids(include_protonated=False): | |
molecules = dict() | |
molecules['GLY'] = 'NCC(=O)O' | |
molecules['ALA'] = 'NC(C)C(=O)O' | |
molecules['SER'] = 'NC(CO)C(=O)O' | |
molecules['THR'] = 'NC(C(C)O)C(=O)O' | |
molecules['CYS'] = 'NC(CS)C(=O)O' | |
molecules['VAL'] = 'NC(C(C)C)C(=O)O' | |
molecules['LEU'] = 'NC(CC(C)C)C(=O)O' | |
molecules['ILE'] = 'NC(C(C)CC)C(=O)O' |
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#!/usr/bin/env bash | |
TRAJIN=traj.xtc | |
TRAJOUT=trajfin.xtc | |
# delete the trajectory so gromacs wont display silly backup messages | |
if [ -e $TRAJOUT ] | |
then | |
rm -f $TRAJOUT | |
fi |
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