def calc_new(self, coords, dirname):
try:
from forcebalance.gmxio import GMX
except ImportError:
raise ImportError(
"ForceBalance is needed to compute energies and gradients using Gromacs."
)
if not os.path.exists(dirname): os.makedirs(dirname)
try:
Gro = Molecule("conf.gro")
Gro.xyzs[0] = coords.reshape(-1, 3) * bohr2ang
cwd = os.getcwd()
shutil.copy2("topol.top", dirname)
shutil.copy2("shot.mdp", dirname)
os.chdir(dirname)
Gro.write("coords.gro")
G = GMX(coords="coords.gro",
gmx_top="topol.top",
gmx_mdp="shot.mdp")
EF = G.energy_force()
Energy = EF[0, 0] / eqcgmx
Gradient = EF[0, 1:] / fqcgmx
os.chdir(cwd)
except (OSError, IOError, RuntimeError, subprocess.CalledProcessError):
raise GromacsEngineError
return {'energy': Energy, 'gradient': Gradient}
def calc_new(self, coords, dirname):
if not os.path.exists(dirname): os.makedirs(dirname)
Gro = Molecule("conf.gro")
Gro.xyzs[0] = coords.reshape(-1, 3) * 0.529
cwd = os.getcwd()
shutil.copy2("topol.top", dirname)
shutil.copy2("shot.mdp", dirname)
os.chdir(dirname)
Gro.write("coords.gro")
G = GMX(coords="coords.gro", gmx_top="topol.top", gmx_mdp="shot.mdp")
EF = G.energy_force()
Energy = EF[0, 0] / eqcgmx
Gradient = EF[0, 1:] / fqcgmx
os.chdir(cwd)
return Energy, Gradient
def setup_class(cls):
"""
setup any state specific to the execution of the given class (which usually contains tests).
"""
super(TestAmber99SB, cls).setup_class()
tinkerpath = which('testgrad')
# try to find mdrun_d or gmx_d
# gmx should be built with config -DGMX_DOUBLE=ON
gmxpath = which('mdrun_d') or which('gmx_d')
gmxsuffix = '_d'
# Tests will FAIL if use single precision gromacs
# gmxpath = which('mdrun') or which('gmx')
# gmxsuffix = ''
# self.logger.debug("\nBuilding options for target...\n")
cls.cwd = os.path.dirname(os.path.realpath(__file__))
os.chdir(os.path.join(cls.cwd, "files", "amber_alaglu"))
cls.tmpfolder = os.path.join(cls.cwd, "files", "amber_alaglu", "temp")
if not os.path.exists(cls.tmpfolder):
os.makedirs(cls.tmpfolder)
os.chdir(cls.tmpfolder)
for i in [
"topol.top", "shot.mdp", "a99sb.xml", "a99sb.prm", "all.gro",
"all.arc", "AceGluNme.itp", "AceAlaNme.itp", "a99sb.itp"
]:
os.system("ln -fs ../%s" % i)
cls.engines = OrderedDict()
# Set up GMX engine
if gmxpath != '':
cls.engines['GMX'] = GMX(coords="all.gro",
gmx_top="topol.top",
gmx_mdp="shot.mdp",
gmxpath=gmxpath,
gmxsuffix=gmxsuffix)
else:
logger.warn("GROMACS cannot be found, skipping GMX tests.")
# Set up TINKER engine
if tinkerpath != '':
cls.engines['TINKER'] = TINKER(coords="all.arc",
tinker_key="alaglu.key",
tinkerpath=tinkerpath)
else:
logger.warn("TINKER cannot be found, skipping TINKER tests.")
# Set up OpenMM engine
try:
try:
import openmm
except ImportError:
import simtk.openmm
cls.engines['OpenMM'] = OpenMM(coords="all.gro",
pdb="conf.pdb",
ffxml="a99sb.xml",
platname="Reference",
precision="double")
except:
logger.warn("OpenMM cannot be imported, skipping OpenMM tests.")
def calc_new(self, coords, dirname):
try:
from forcebalance.gmxio import GMX
except ImportError:
raise ImportError("ForceBalance is needed to compute energies and gradients using Gromacs.")
if not os.path.exists(dirname): os.makedirs(dirname)
try:
Gro = Molecule("conf.gro")
Gro.xyzs[0] = coords.reshape(-1,3) * bohr2ang
cwd = os.getcwd()
shutil.copy2("topol.top", dirname)
shutil.copy2("shot.mdp", dirname)
os.chdir(dirname)
Gro.write("coords.gro")
G = GMX(coords="coords.gro", gmx_top="topol.top", gmx_mdp="shot.mdp")
EF = G.energy_force()
Energy = EF[0, 0] / eqcgmx
Gradient = EF[0, 1:] / fqcgmx
os.chdir(cwd)
except (OSError, IOError, RuntimeError, subprocess.CalledProcessError):
raise GromacsEngineError
return {'energy':Energy, 'gradient':Gradient}
def setUp(self):
tinkerpath = which('testgrad')
gmxsuffix = '_d'
gmxpath = which('mdrun' + gmxsuffix)
self.logger.debug("\nBuilding options for target...\n")
self.cwd = os.getcwd()
os.chdir(os.path.join(os.getcwd(), "test", "files", "amber_alaglu"))
if not os.path.exists("temp"): os.makedirs("temp")
os.chdir("temp")
for i in [
"topol.top", "shot.mdp", "a99sb.xml", "a99sb.prm", "all.gro",
"all.arc", "AceGluNme.itp", "AceAlaNme.itp", "a99sb.itp"
]:
os.system("ln -fs ../%s" % i)
self.engines = OrderedDict()
# Set up GMX engine
if gmxpath != '':
self.engines['GMX'] = GMX(coords="all.gro",
gmx_top="topol.top",
gmx_mdp="shot.mdp",
gmxpath=gmxpath,
gmxsuffix=gmxsuffix)
else:
logger.warn("GROMACS cannot be found, skipping GMX tests.")
# Set up TINKER engine
if tinkerpath != '':
self.engines['TINKER'] = TINKER(coords="all.arc",
tinker_key="alaglu.key",
tinkerpath=tinkerpath)
else:
logger.warn("TINKER cannot be found, skipping TINKER tests.")
# Set up OpenMM engine
openmm = False
try:
import simtk.openmm
openmm = True
except:
logger.warn("OpenMM cannot be imported, skipping OpenMM tests.")
if openmm:
self.engines['OpenMM'] = OpenMM(coords="all.gro",
pdb="conf.pdb",
ffxml="a99sb.xml",
platname="Reference",
precision="double")
self.addCleanup(os.system, 'cd .. ; rm -rf temp')
