.. _refBernetti2020:
-:sup:`184` Bernetti, M. and Bussi, G.,
+:sup:`184` Bernetti, M. and Bussi G.,
"Pressure control using stochastic cell rescaling", *J. Chem. Phys.*, **153**, 114107 (2020).
+.. raw:: html
+
+ </div>
+
+ <div id="ref-Lidmar2012">
+
+.. _refLidmar2012:
+
+:sup:`185` Lidmar J.,
+"Improving the efficiency of extended ensemble simulations: The accelerated weight histogram method", *Phys. Rev. E*, **85**, 0256708 (2012).
+
+.. raw:: html
+
+ </div>
+
+ <div id="ref-Lindahl2018">
+
+.. _refLindahl2018:
+
+:sup:`186` Lindahl V., Lidmar J. and Hess B.,
+"Riemann metric approach to optimal sampling of multidimensional free-energy landscapes", *Phys. Rev. E*, **98**, 023312 (2018).
+
+.. raw:: html
+
+ </div>
+
+ <div id="ref-LundBorg2021">
+
+.. _refLundborg2021:
+
+:sup:`187` Lundborg M., Lidmar J. and Hess B.,
+"The accelerated weight histogram method for alchemical free energy calculations", *J. Chem. Phys.*, **154**, 204103 (2021).
+
.. raw:: html
</div>
Adaptive biasing with AWH
-------------------------
-The accelerated weight histogram method
+The accelerated weight histogram method :ref:`185 <refLidmar2012>`
:ref:`137 <reflindahl2014accelerated>` calculates the PMF along a reaction coordinate by adding
an adaptively determined biasing potential. AWH flattens free energy
barriers along the reaction coordinate by applying a history-dependent
toward :math:`\rho(\lambda)`.
It is also possible to directly control the :math:`\lambda` state
-of, e.g., alchemical free energy perturbations. In that case there is no harmonic
+of, e.g., alchemical free energy perturbations :ref:`187 <reflundborg2021>`. In that case there is no harmonic
potential and :math:`\lambda` changes in discrete steps along the reaction coordinate
depending on the biased free energy difference between the :math:`\lambda` states.
N.b., it is not yet possible to use AWH in combination with perturbed masses or
is the deviation of the force. The factors :math:`\omega(\lambda|x(t))`,
see :eq:`Eq %s <eqawhomega>`, reweight the samples.
:math:`\eta_{\mu\nu}(\lambda)` is a friction
-tensor \ :ref:`144 <refsivak2012thermodynamic>`. Its matrix elements are inversely proportional to local
+tensor :ref:`186 <reflindahl2018>` and :ref:`144 <refsivak2012thermodynamic>`. Its matrix elements are inversely proportional to local
diffusion coefficients. A measure of sampling (in)efficiency at each
:math:`\lambda` is given by
molecules.
- **AWH code:** currently acts on coordinates provided by the pull
- code.
+ code or the free-energy lambda parameter.
- **free-energy code with harmonic bonds or constraints:** between
single atoms.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Here AWH can be extended to work on other coordinates than pull. */
};
-/*! \brief Checks whether any dimension uses pulling as a coordinate provider.
+/*! \brief Checks whether any dimension uses the given coordinate provider type.
*
* \param[in] awhBiasParams The bias params to check.
- * \returns true if any dimension of the bias is linked to pulling.
+ * \param[in] awhCoordProvider The type of coordinate provider
+ * \returns true if any dimension of the bias is linked to the given provider
*/
-static bool anyDimUsesPull(const AwhBiasParams& awhBiasParams)
+static bool anyDimUsesProvider(const AwhBiasParams& awhBiasParams, const int awhCoordProvider)
{
for (int d = 0; d < awhBiasParams.ndim; d++)
{
const AwhDimParams& awhDimParams = awhBiasParams.dimParams[d];
- if (awhDimParams.eCoordProvider == eawhcoordproviderPULL)
+ if (awhDimParams.eCoordProvider == awhCoordProvider)
{
return true;
}
return false;
}
-/*! \brief Checks whether any dimension uses pulling as a coordinate provider.
+/*! \brief Checks whether any dimension uses the given coordinate provider type.
*
* \param[in] awhParams The AWH params to check.
- * \returns true if any dimension of awh is linked to pulling.
+ * \param[in] awhCoordProvider The type of coordinate provider
+ * \returns true if any dimension of awh is linked to the given provider type.
*/
-static bool anyDimUsesPull(const AwhParams& awhParams)
+static bool anyDimUsesProvider(const AwhParams& awhParams, const int awhCoordProvider)
{
for (int k = 0; k < awhParams.numBias; k++)
{
const AwhBiasParams& awhBiasParams = awhParams.awhBiasParams[k];
- if (anyDimUsesPull(awhBiasParams))
+ if (anyDimUsesProvider(awhBiasParams, awhCoordProvider))
{
return true;
}
numFepLambdaStates_(numFepLambdaStates),
fepLambdaState_(fepLambdaState)
{
- if (anyDimUsesPull(awhParams))
+ if (anyDimUsesProvider(awhParams, eawhcoordproviderPULL))
{
GMX_RELEASE_ASSERT(inputRecord.pull != nullptr, "With AWH we should have pull parameters");
GMX_RELEASE_ASSERT(pull_work != nullptr,
if (fplog != nullptr)
{
please_cite(fplog, "Lindahl2014");
+
+ if (anyDimUsesProvider(awhParams, eawhcoordproviderFREE_ENERGY_LAMBDA))
+ {
+ please_cite(fplog, "Lundborg2021");
+ }
}
if (haveBiasSharingWithinSimulation(awhParams))
void Awh::registerAwhWithPull(const AwhParams& awhParams, pull_t* pull_work)
{
- GMX_RELEASE_ASSERT(!anyDimUsesPull(awhParams) || pull_work, "Need a valid pull object");
+ GMX_RELEASE_ASSERT(!anyDimUsesProvider(awhParams, eawhcoordproviderPULL) || pull_work,
+ "Need a valid pull object");
for (int k = 0; k < awhParams.numBias; k++)
{
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{ "Bernetti2020", "M. Bernetti, G. Bussi",
"Pressure control using stochastic cell rescaling", "J. Chem. Phys.", 153, 2020,
"114107" },
+ { "Lundborg2021", "M. Lundborg, J. Lidmar, B. Hess",
+ "The accelerated weight histogram method for alchemical free energy calculations",
+ "J. Chem. Phys.", 154, 2021, "204103" },
};
#define NSTR static_cast<int>(asize(citedb))
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff