National Institute of Advanced Industrial Science and Technology (AIST), Japan.
This file contains module for LogMFD method proposed by Tetsuya Morishita(AIST).
then written by Mizuho information and Research Institute, Inc.
The LogMFD module is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
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@@ -151,7 +150,7 @@ With the MF evaluated using the PD approach, reconstructing free energy profiles
Note that LogPD calculations should always be initiated with an equilibrium \f${\bf q}\f$-configuration in each replica, because the Crooks-Jarzynski non-equilibrium work relation is invoked. Also note that LogPD is currently available only with Gromacs, while LogMFD can be performed with LAMMPS, Gromacs, and NAMD.
\section Thermostat Using LogMFD with a thermostat /PD
\section Thermostat Using LogMFD/PD with a thermostat
Introducing a thermostat on \f${\bf X}\f$ is often recommended in LogMFD/PD to maintain the adiabatic decoupling between \f${\bf q}\f$ and \f${\bf X}\f$. In the framework of the LogMFD approach, the Nose-Hoover type thermostat and the Gaussian isokinetic (velocity scaling) thermostat can be used to control the kinetic energy of \f${\bf X}\f$.
