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Merge pull request #10 from fjclark/feature_lj_cor
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Add LJ Correction Test

I'm accepting this and am now in the process of merging your changes into `openbiosim/sire:devel`. I'll let you know once it is ready :-)
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@chryswoods
chryswoods authored Jan 17, 2023
2 parents b782f8e + 1c42461 commit fe48a8f
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37 changes: 37 additions & 0 deletions unittests/Tools/test_lj_cor.py
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####################################################################################################
# #
# Sire script to test that LJ correction works correctly #
# #
####################################################################################################


try:
import sire
sire.use_old_api()
except ImportError:
pass

from Sire.Tools import LJcutoff
from Sire.Tools import readParams
from Sire.Units import *

from nose.tools import assert_almost_equal

params = {}
params = readParams("../io/lj_cor/sim.cfg")

def test_lj_cor(verbose=False):
"""Check that LJ correction gives expected dG and SD"""

dg, _ = LJcutoff.runLambda(params) # Ignore SD as this will be 0 for single frame

if verbose:
print("#######################################")
print("Testing LJ Correction...")
print(f"LJ correction deltaG = {dg}")
print("#######################################")

assert_almost_equal(dg.value(), -428.6141143872228)

if __name__ == '__main__':
test_lj_cor(True)
309 changes: 309 additions & 0 deletions unittests/io/lj_cor/MORPH.vanish.pert
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version 1
molecule LIG
atom
name CAB
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAC
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAD
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAE
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAF
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAG
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAH
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAI
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAJ
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAK
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAL
initial_type cc
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAP
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAQ
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAR
initial_type cd
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAS
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAT
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name CAU
initial_type ca
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.31521 0.09880
final_LJ 0.00000 0.00000
endatom
atom
name NAM
initial_type nd
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.38417 0.09410
final_LJ 0.00000 0.00000
endatom
atom
name NAN
initial_type nc
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.38417 0.09410
final_LJ 0.00000 0.00000
endatom
atom
name NAO
initial_type nb
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.38417 0.09410
final_LJ 0.00000 0.00000
endatom
atom
name NAV
initial_type na
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.20581 0.20420
final_LJ 0.00000 0.00000
endatom
atom
name OAA
initial_type oh
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 3.24287 0.09300
final_LJ 0.00000 0.00000
endatom
atom
name H01
initial_type ha
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.62548 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H02
initial_type ha
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.62548 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H03
initial_type ha
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.62548 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H04
initial_type ha
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.62548 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H05
initial_type ha
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.62548 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H06
initial_type ha
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.62548 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H07
initial_type ha
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.62548 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H08
initial_type ha
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.62548 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H09
initial_type ha
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.62548 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H10
initial_type ha
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.62548 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H11
initial_type h4
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 2.53639 0.01610
final_LJ 0.00000 0.00000
endatom
atom
name H12
initial_type ho
final_type du
initial_charge 0.00000
final_charge 0.00000
initial_LJ 0.53792 0.00470
final_LJ 0.00000 0.00000
endatom
end molecule
27 changes: 27 additions & 0 deletions unittests/io/lj_cor/sim.cfg
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morphfile = ../io/lj_cor/MORPH.vanish.pert
trajfile = ../io/lj_cor/traj.dcd
topfile = ../io/receptor_ligand_restraints/SYSTEM.top
crdfile = ../io/receptor_ligand_restraints/SYSTEM.crd
perturbed residue number = 1
nmoves = 25000
ncycles = 80
buffered coordinates frequency = 5000
save coordinates = True
timestep = 4 * femtosecond
constraint = allbonds
hydrogen mass repartitioning factor = 4.0
cutoff type = cutoffperiodic
cutoff distance = 12*angstrom
barostat = True
andersen = True
energy frequency = 100
precision = mixed
minimise = True
equilibrate = False
equilibration iterations = 5000
center solute = True
reaction field dielectric = 78.3
minimal coordinate saving = False
lambda array = 0.000, 0.025, 0.050, 0.075, 0.100, 0.125, 0.150, 0.175, 0.200, 0.225, 0.250, 0.275, 0.300, 0.325, 0.350, 0.375, 0.400, 0.425, 0.450, 0.475, 0.500, 0.525, 0.550, 0.575, 0.600, 0.625, 0.650, 0.675, 0.700, 0.725, 0.750, 0.800, 0.850, 0.900, 0.950, 1.000
use boresch restraints = True
boresch restraints dictionary = {"anchor_points":{"r1":4946, "r2":4944, "r3":4949, "l1":11, "l2":2, "l3":3},"equilibrium_values":{"r0":5.92, "thetaA0":1.85, "thetaB0":1.59,"phiA0":-0.30, "phiB0":-1.55, "phiC0":2.90},"force_constants":{"kr":25.49, "kthetaA":66.74, "kthetaB":38.39, "kphiA":215.36, "kphiB":49.23, "kphiC":49.79}}
Binary file added unittests/io/lj_cor/traj.dcd
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