nomad-parser-plugins-atomistic 1.0__py3-none-any.whl

atomisticparsers/gromacs/metainfo/gromacs.py

@@ -0,0 +1,2388 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+import numpy as np  # pylint: disable=unused-import
+import typing  # pylint: disable=unused-import
+from nomad.metainfo import (  # pylint: disable=unused-import
+    MSection,
+    MCategory,
+    Category,
+    Package,
+    Quantity,
+    Section,
+    SubSection,
+    SectionProxy,
+)
+import runschema.run  # pylint: disable=unused-import
+import runschema.calculation  # pylint: disable=unused-import
+import runschema.method  # pylint: disable=unused-import
+import runschema.system  # pylint: disable=unused-import
+import simulationworkflowschema
+
+
+m_package = Package()
+
+
+class x_gromacs_mdin_input_output_files(MCategory):
+    """
+    Parameters of mdin belonging to x_gromacs_section_control_parameters.
+    """
+
+    m_def = Category()
+
+
+class x_gromacs_mdin_control_parameters(MCategory):
+    """
+    Parameters of mdin belonging to x_gromacs_section_control_parameters.
+    """
+
+    m_def = Category()
+
+
+class x_gromacs_mdin_method(MCategory):
+    """
+    Parameters of mdin belonging to section method.
+    """
+
+    m_def = Category()
+
+
+class x_gromacs_mdout_single_configuration_calculation(MCategory):
+    """
+    Parameters of mdout belonging to section_single_configuration_calculation.
+    """
+
+    m_def = Category()
+
+
+class x_gromacs_mdout_method(MCategory):
+    """
+    Parameters of mdin belonging to section method.
+    """
+
+    m_def = Category()
+
+
+class x_gromacs_mdout_run(MCategory):
+    """
+    Parameters of mdin belonging to settings run.
+    """
+
+    m_def = Category()
+
+
+class x_gromacs_mdin_run(MCategory):
+    """
+    Parameters of mdin belonging to settings run.
+    """
+
+    m_def = Category()
+
+
+class x_gromacs_section_input_output_files(MSection):
+    """
+    Section to store input and output file names
+    """
+
+    m_def = Section(
+        validate=False,
+    )
+
+    x_gromacs_inout_file_topoltpr = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs input topology file.
+        """,
+    )
+
+    x_gromacs_inout_file_trajtrr = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs input trajectory file.
+        """,
+    )
+
+    x_gromacs_inout_file_trajcompxtc = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs input compressed trajectory file.
+        """,
+    )
+
+    x_gromacs_inout_file_statecpt = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs input coordinates and state file.
+        """,
+    )
+
+    x_gromacs_inout_file_confoutgro = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs output configuration file.
+        """,
+    )
+
+    x_gromacs_inout_file_eneredr = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs output energies file.
+        """,
+    )
+
+
+class x_gromacs_section_control_parameters(MSection):
+    """
+    Section to store the input and output control parameters
+    """
+
+    m_def = Section(
+        validate=False,
+    )
+
+    x_gromacs_inout_control_gromacs_version = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_precision = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_memory_model = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_mpi_library = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_openmp_support = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_gpu_support = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_opencl_support = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_invsqrt_routine = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_simd_instructions = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_fft_library = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_rdtscp_usage = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_cxx11_compilation = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_tng_support = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_tracing_support = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_built_on = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_built_by = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_build_osarch = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_build_cpu_vendor = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_build_cpu_brand = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_build_cpu_family = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_build_cpu_features = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_c_compiler = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_c_compiler_flags = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_cxx_compiler = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_cxx_compiler_flags = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_boost_version = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_integrator = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_tinit = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_dt = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nsteps = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_initstep = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_simulationpart = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_commmode = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstcomm = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_bdfric = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ldseed = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_emtol = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_emstep = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_niter = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_fcstep = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstcgsteep = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nbfgscorr = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_rtpi = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstxout = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstvout = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstfout = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstlog = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstcalcenergy = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstenergy = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstxoutcompressed = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_compressedxprecision = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_cutoffscheme = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstlist = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstype = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_pbc = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_periodicmolecules = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_verletbuffertolerance = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_rlist = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_rlistlong = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstcalclr = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_coulombtype = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_coulombmodifier = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_rcoulombswitch = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_rcoulomb = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_epsilonr = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_epsilonrf = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_vdwtype = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_vdwmodifier = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_rvdwswitch = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_rvdw = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_dispcorr = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_tableextension = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_fourierspacing = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_fouriernx = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_fourierny = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_fouriernz = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_pmeorder = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ewaldrtol = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ewaldrtollj = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ljpmecombrule = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ewaldgeometry = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_epsilonsurface = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_implicitsolvent = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_gbalgorithm = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstgbradii = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_rgbradii = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_gbepsilonsolvent = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_gbsaltconc = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_gbobcalpha = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_gbobcbeta = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_gbobcgamma = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_gbdielectricoffset = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_saalgorithm = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_sasurfacetension = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_tcoupl = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nsttcouple = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nhchainlength = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_printnosehooverchainvariables = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_pcoupl = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_pcoupltype = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstpcouple = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_taup = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_compressibility = Quantity(
+        type=np.float64,
+        shape=[3, 3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_compressibility0 = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_compressibility1 = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_compressibility2 = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_refp = Quantity(
+        type=np.float64,
+        shape=[3, 3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_refp0 = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_refp1 = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_refp2 = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_refcoordscaling = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_posrescom = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_posrescom0 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_posrescom1 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_posrescom2 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_posrescomb = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_posrescomb0 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_posrescomb1 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_posrescomb2 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_qmmm = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_qmconstraints = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_qmmmscheme = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_mmchargescalefactor = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ngqm = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_constraintalgorithm = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_continuation = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_shakesor = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_shaketol = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_lincsorder = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_lincsiter = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_lincswarnangle = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nwall = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_walltype = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_wallrlinpot = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_wallatomtype = Quantity(
+        type=np.float64,
+        shape=[2],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_wallatomtype0 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_wallatomtype1 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_walldensity = Quantity(
+        type=np.float64,
+        shape=['*'],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_walldensity0 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_walldensity1 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_wallewaldzfac = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_pull = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_rotation = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_interactivemd = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_disre = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_disreweighting = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_disremixed = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_drfc = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_drtau = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstdisreout = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_orirefc = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_oriretau = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nstorireout = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_freeenergy = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_cosacceleration = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_deform = Quantity(
+        type=np.float64,
+        shape=[3, 3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_deform0 = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_deform1 = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_deform2 = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_simulatedtempering = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ex = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ext = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ey = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_eyt = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ez = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_ezt = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_swapcoords = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_adress = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_userint1 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_userint2 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_userint3 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_userint4 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_userreal1 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_userreal2 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_userreal3 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_userreal4 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nrdf = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_reft = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_taut = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_annealing = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_annealingnpoints = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_acc = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_nfreeze = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_energygrpflags = Quantity(
+        type=np.float64,
+        shape=[3, 2],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_energygrpflags0 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_energygrpflags1 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+    x_gromacs_inout_control_energygrpflags2 = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs running environment and control parameters.
+        """,
+    )
+
+
+class x_gromacs_section_atom_to_atom_type_ref(MSection):
+    """
+    Section to store atom label to atom type definition list
+    """
+
+    m_def = Section(
+        validate=False,
+    )
+
+    x_gromacs_atom_to_atom_type_ref = Quantity(
+        type=np.int64,
+        shape=['number_of_atoms_per_type'],
+        description="""
+        Reference to the atoms of each atom type.
+        """,
+    )
+
+
+class x_gromacs_section_single_configuration_calculation(MSection):
+    """
+    section for gathering values for MD steps
+    """
+
+    m_def = Section(
+        validate=False,
+    )
+
+
+class System(runschema.system.System):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_gromacs_atom_positions_image_index = Quantity(
+        type=np.int32,
+        shape=['number_of_atoms', 3],
+        unit='dimensionless',
+        description="""
+        PBC image flag index.
+        """,
+    )
+
+    x_gromacs_atom_positions_scaled = Quantity(
+        type=np.float64,
+        shape=['number_of_atoms', 3],
+        unit='dimensionless',
+        description="""
+        Position of the atoms in a scaled format [0, 1].
+        """,
+    )
+
+    x_gromacs_atom_positions_wrapped = Quantity(
+        type=np.float64,
+        shape=['number_of_atoms', 3],
+        unit='meter',
+        description="""
+        Position of the atoms wrapped back to the periodic box.
+        """,
+    )
+
+    x_gromacs_lattice_lengths = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Lattice dimensions in a vector. Vector includes [a, b, c] lengths.
+        """,
+    )
+
+    x_gromacs_lattice_angles = Quantity(
+        type=np.float64,
+        shape=[3],
+        description="""
+        Angles of lattice vectors. Vector includes [alpha, beta, gamma] in degrees.
+        """,
+    )
+
+    x_gromacs_dummy = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        dummy
+        """,
+    )
+
+    x_gromacs_mdin_finline = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        finline in mdin
+        """,
+    )
+
+    x_gromacs_traj_timestep_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_traj_number_of_atoms_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_traj_box_bound_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_traj_box_bounds_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_traj_variables_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_traj_atoms_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+
+class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_gromacs_barostat_target_pressure = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='pascal',
+        description="""
+        MD barostat target pressure.
+        """,
+    )
+
+    x_gromacs_barostat_tau = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        MD barostat relaxation time.
+        """,
+    )
+
+    x_gromacs_barostat_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        MD barostat type, valid values are defined in the barostat_type wiki page.
+        """,
+    )
+
+    x_gromacs_integrator_dt = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        MD integration time step.
+        """,
+    )
+
+    x_gromacs_integrator_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        MD integrator type, valid values are defined in the integrator_type wiki page.
+        """,
+    )
+
+    x_gromacs_periodicity_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Periodic boundary condition type in the sampling (non-PBC or PBC).
+        """,
+    )
+
+    x_gromacs_langevin_gamma = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        Langevin thermostat damping factor.
+        """,
+    )
+
+    x_gromacs_number_of_steps_requested = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Number of requested MD integration time steps.
+        """,
+    )
+
+    x_gromacs_thermostat_level = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        MD thermostat level (see wiki: single, multiple, regional).
+        """,
+    )
+
+    x_gromacs_thermostat_target_temperature = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='kelvin',
+        description="""
+        MD thermostat target temperature.
+        """,
+    )
+
+    x_gromacs_thermostat_tau = Quantity(
+        type=np.float64,
+        shape=[],
+        unit='second',
+        description="""
+        MD thermostat relaxation time.
+        """,
+    )
+
+    x_gromacs_thermostat_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        MD thermostat type, valid values are defined in the thermostat_type wiki page.
+        """,
+    )
+
+
+class AtomParameters(runschema.method.AtomParameters):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_gromacs_atom_name = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Atom name of an atom in topology definition.
+        """,
+    )
+
+    x_gromacs_atom_type = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Atom type of an atom in topology definition.
+        """,
+    )
+
+    x_gromacs_atom_element = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Atom type of an atom in topology definition.
+        """,
+    )
+
+    x_gromacs_atom_type_element = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Element symbol of an atom type.
+        """,
+    )
+
+    x_gromacs_atom_type_radius = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        van der Waals radius of an atom type.
+        """,
+    )
+
+    number_of_atoms_per_type = Quantity(
+        type=int,
+        shape=[],
+        description="""
+        Number of atoms involved in this type.
+        """,
+    )
+
+    x_gromacs_atom_resid = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_gromacs_atom_resname = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_gromacs_atom_molnum = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        """,
+    )
+
+    x_gromacs_atom_moltype = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        """,
+    )
+
+
+class Interaction(runschema.method.Interaction):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_gromacs_interaction_atom_to_atom_type_ref = Quantity(
+        type=runschema.method.AtomParameters,
+        shape=['number_of_atoms_per_interaction'],
+        description="""
+        Reference to the atom type of each interaction atoms.
+        """,
+    )
+
+    x_gromacs_number_of_defined_pair_interactions = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        Number of defined pair interactions (L-J pairs).
+        """,
+    )
+
+    x_gromacs_pair_interaction_atom_type_ref = Quantity(
+        type=runschema.method.AtomParameters,
+        shape=[
+            'x_gromacs_number_of_defined_pair_interactions',
+            'number_of_atoms_per_interaction',
+        ],
+        description="""
+        Reference to the atom type for pair interactions.
+        """,
+    )
+
+    x_gromacs_pair_interaction_parameters = Quantity(
+        type=np.float64,
+        shape=['x_gromacs_number_of_defined_pair_interactions', 2],
+        description="""
+        Pair interactions parameters.
+        """,
+    )
+
+    x_gromacs_molecule_interaction_atom_to_atom_type_ref = Quantity(
+        type=runschema.method.AtomParameters,
+        shape=['number_of_atoms_per_interaction'],
+        description="""
+        Reference to the atom type of each molecule interaction atoms.
+        """,
+    )
+
+    x_gromacs_number_of_defined_molecule_pair_interactions = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        Number of defined pair interactions within a molecule (L-J pairs).
+        """,
+    )
+
+    x_gromacs_pair_molecule_interaction_parameters = Quantity(
+        type=np.float64,
+        shape=['number_of_defined_molecule_pair_interactions', 2],
+        description="""
+        Molecule pair interactions parameters.
+        """,
+    )
+
+    x_gromacs_pair_molecule_interaction_to_atom_type_ref = Quantity(
+        type=runschema.method.AtomParameters,
+        shape=[
+            'x_gromacs_number_of_defined_pair_interactions',
+            'number_of_atoms_per_interaction',
+        ],
+        description="""
+        Reference to the atom type for pair interactions within a molecule.
+        """,
+    )
+
+
+class Run(runschema.run.Run):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_gromacs_program_version_date = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Program version date.
+        """,
+    )
+
+    x_gromacs_parallel_task_nr = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Program task no.
+        """,
+    )
+
+    x_gromacs_number_of_tasks = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Number of tasks in parallel program (MPI).
+        """,
+    )
+
+    x_gromacs_program_module_version = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs program module (gmx) version.
+        """,
+    )
+
+    x_gromacs_program_license = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Gromacs program license.
+        """,
+    )
+
+    x_gromacs_xlo_xhi = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        test
+        """,
+    )
+
+    x_gromacs_data_file_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Filename of data file
+        """,
+    )
+
+    x_gromacs_program_working_path = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_program_execution_host = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_program_execution_path = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_program_module = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_program_execution_date = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_program_execution_time = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_mdin_header = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_mdin_wt = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_section_input_output_files = SubSection(
+        sub_section=SectionProxy('x_gromacs_section_input_output_files'), repeats=False
+    )
+
+    x_gromacs_section_control_parameters = SubSection(
+        sub_section=SectionProxy('x_gromacs_section_control_parameters'), repeats=False
+    )
+
+
+class Constraint(runschema.system.Constraint):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_gromacs_input_units_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        It determines the units of all quantities specified in the input script and data
+        file, as well as quantities output to the screen, log file, and dump files.
+        """,
+    )
+
+    x_gromacs_data_bond_types_store = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        store temporarly
+        """,
+    )
+
+    x_gromacs_data_bond_count_store = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        store temporarly
+        """,
+    )
+
+    x_gromacs_data_angle_count_store = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        store temporarly
+        """,
+    )
+
+    x_gromacs_data_atom_types_store = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        store temporarly
+        """,
+    )
+
+    x_gromacs_data_dihedral_count_store = Quantity(
+        type=np.int32,
+        shape=[],
+        description="""
+        store temporarly
+        """,
+    )
+
+    x_gromacs_data_angles_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        store temporarly
+        """,
+    )
+
+    x_gromacs_data_angle_list_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_data_bond_list_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_data_dihedral_list_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_data_dihedral_coeff_list_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_masses_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_data_topo_list_store = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        tmp
+        """,
+    )
+
+    x_gromacs_section_atom_to_atom_type_ref = SubSection(
+        sub_section=SectionProxy('x_gromacs_section_atom_to_atom_type_ref'),
+        repeats=True,
+    )
+
+
+class CalcEntry(MSection):
+    """
+    Section describing a general type of calculation.
+    """
+
+    m_def = Section(validate=False)
+
+    kind = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Kind of the quantity.
+        """,
+    )
+
+    value = Quantity(
+        type=np.float64,
+        shape=[],
+        description="""
+        Value of this contribution.
+        """,
+    )
+
+    unit = Quantity(
+        type=str,
+        shape=[],
+        description="""
+        Unit of the parameter as a string.
+        """,
+    )
+
+
+class Calculation(runschema.calculation.Calculation):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_gromacs_section_single_configuration_calculation = SubSection(
+        sub_section=SectionProxy('x_gromacs_section_single_configuration_calculation'),
+        repeats=True,
+    )
+
+    x_gromacs_thermodynamics_contributions = SubSection(
+        sub_section=CalcEntry.m_def,
+        description="""
+        Contains other gromacs-specific thermodynamic and energy contributions that are not already defined.
+        """,
+        repeats=True,
+    )
+
+
+class Energy(runschema.calculation.Energy):
+    m_def = Section(
+        validate=False,
+        extends_base_section=True,
+    )
+
+    x_gromacs_energy_contributions = SubSection(
+        sub_section=runschema.calculation.EnergyEntry.m_def,
+        description="""
+        Contains other gromacs-specific energy contributions that are not already defined.
+        """,
+        repeats=True,
+    )