Gromacs  2020.4
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
List of all members | Public Member Functions | Public Attributes
gmx::test::DensityFittingTest Class Reference
+ Inheritance diagram for gmx::test::DensityFittingTest:
+ Collaboration diagram for gmx::test::DensityFittingTest:

Description

End to end test for the density fitting functionality in mdrun.

This test checks whether the density fitting related .mdp input options are understood by grompp and that the density fitting module in mdrun computes the correct density fitting energies and stores them in the .edr output file.

Public Member Functions

void checkMdrun (real energyTermMagnitude)
 Check the output of mdrun.
 

Public Attributes

const std::string mdpEminDensfitYesUnsetValues
 Mdp values for steepest-decent energy minimization with default density fitting parameters. More...
 
const std::string mdpMdDensfitYesUnsetValues
 Mdp values for md integrator with default density fitting parameters. More...
 
const std::string mdpDensiftAllDefaultsChanged_
 Mdp values for steepest-decent energy minimization with density fitting values set to non-defaults. More...
 
const std::string mdpEnergyAndDensityfittingIntervalMismatch_
 Set mdp values so that energy calculation interval and density guided simulation interval mismatch. More...
 
const std::string mdpSkipDensityfittingEveryOtherStep_
 Set mdp values so that we skip every other step. More...
 
CommandLine commandLineForMdrun_
 The command line to call mdrun.
 
- Public Attributes inherited from gmx::test::MdrunTestFixture
TestFileManager fileManager_
 Manages temporary files during the test.
 
SimulationRunner runner_
 Helper object to manage the preparation for and call of mdrun.
 

Member Data Documentation

const std::string gmx::test::DensityFittingTest::mdpDensiftAllDefaultsChanged_
Initial value:
"density-guided-simulation-similarity-measure = relative-entropy\n"
"density-guided-simulation-atom-spreading-weight = mass\n"
"density-guided-simulation-force-constant = -1\n"
"density-guided-simulation-gaussian-transform-spreading-width = 0.8\n"
"density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width = "
"6\n"
"density-guided-simulation-normalize-densities = false\n")

Mdp values for steepest-decent energy minimization with density fitting values set to non-defaults.

const std::string gmx::test::DensityFittingTest::mdpEminDensfitYesUnsetValues
Initial value:
"integrator = steep\n"
"nsteps = 2\n"
"cutoff-scheme = verlet\n"
"density-guided-simulation-active = yes\n"
"density-guided-simulation-group = FirstThreeOfTwelve\n"
"density-guided-simulation-reference-density-filename = %s\n",
TestFileManager::getInputFilePath("ellipsoid-density.mrc").c_str())

Mdp values for steepest-decent energy minimization with default density fitting parameters.

const std::string gmx::test::DensityFittingTest::mdpEnergyAndDensityfittingIntervalMismatch_
Initial value:
"nstcalcenergy = 7\n"
"density-guided-simulation-nst = 3\n")

Set mdp values so that energy calculation interval and density guided simulation interval mismatch.

const std::string gmx::test::DensityFittingTest::mdpMdDensfitYesUnsetValues
Initial value:
"integrator = md\n"
"nsteps = 2\n"
"cutoff-scheme = verlet\n"
"density-guided-simulation-active = yes\n"
"density-guided-simulation-group = FirstThreeOfTwelve\n"
"density-guided-simulation-reference-density-filename = %s\n",
TestFileManager::getInputFilePath("ellipsoid-density.mrc").c_str())

Mdp values for md integrator with default density fitting parameters.

const std::string gmx::test::DensityFittingTest::mdpSkipDensityfittingEveryOtherStep_
Initial value:
"nstenergy = 2\n"
"density-guided-simulation-nst = 2\n")

Set mdp values so that we skip every other step.


The documentation for this class was generated from the following file: