Merge remote-tracking branch 'origin/v2.5' into fix-spellings

CHANGES/v2.5.md

@@ -13,6 +13,9 @@ Changes from version 2.4 which are relevant for users:
     to set correctly the `LD_LIBRARY_PATH` variable for the linux executable to work correctly. The procedure has been tested well on OSX and Linux,
     but could give problems on other platform. Please report possible problems on the mailing list.
   - \ref driver now stops correctly when using \ref COMMITTOR. If you want to continue the analysis, use the `NOSTOP` flag in \ref COMMITTOR.
+  - \ref METAD the calculation of the reweigthing factor is now activated by CALC_RCT instead of REWEIGHTING_NGRID and REWEIGHTING_NHILLS, the frequency of update can be set 
+    by RCT_USTRIDE, the default value is 1 and should be ok for most of the cases
+  - Fixed sign in Cartesian components of \ref PUCKERING with 6 membered rings (thanks to Carol Simoes and Javi Iglesias).
 
 - New actions:
   - \ref COLLECT_FRAMES
@@ -81,6 +84,8 @@ Changes from version 2.4 which are relevant for users:
   - Implemented bash autocompletion, see \ref BashAutocompletion.
   - \ref MOLINFO now allows selecting atoms from chains with a numeric ID (see \issue{320}).
   - Removed the patch for GMX 5.1.4
+  - LAMMPS patch has been finally removed. Notice that LAMMPS natively supports PLUMED now.
+  - AMBER patch has been finally removed. Notice that AMBER (sander module) natively supports PLUMED starting with version 15.
   - \ref RMSD calculation has been optimized. This should positively affect the performances of CVs where
      many RMSD values are computed on small groups of atoms, such as secondary structure variables.
   - In \ref METAD, when using a bias factor equal to one (no bias) the `rct` component is set to zero rather than to one.
@@ -88,6 +93,7 @@ Changes from version 2.4 which are relevant for users:
   - When using \ref MOLINFO, also the following shortcuts are available for selecting atoms: `@nucleic`, `@protein`, `@water`, `@ions`, `@hydrogens`, `@nonhydrogens`.
   - When using \ref MOLINFO, individual atoms can be chosen also from water molecules (e.g. `@OW-100`).
   - Additional switching function COSINUS contributed by Michael King
+  - added API to set the number of used openMP threads from the linked code, updated gromacs 2018.3 patch to use it
 
 Changes from version 2.4 which are relevant for developers:
 - Code has been cleanup up replacing a number of pointers with `std::unique_ptr`. All `delete` statements
@@ -135,13 +141,9 @@ Changes from version 2.4 which are relevant for developers:
 - Absolute/relative soname/install_name can be configured on linux/OSX. This feature is only
   for testing, the default choice is the typical one used on the respective operating system.
 - On OSX, `plumed` and `libplumed.dylib` will find `libplumedKernel.dylib` using `@loader_path`.
+- Using CXX compiler to link the main program.
+- plumed can be compiled with arrayfire to enable for gpu code. \ref SAXS collective variable is available as part of the isdb module to provide an example of a gpu implementation for a CV
 
 Fixes done after beta (this list will be merged to the one above):
-- (developers) Using CXX compiler to link the main program.
-- (users) added API to set the number of used openMP threads from the linked code, updated gromacs 2018.3 patch to use it
-- (users) Fixed sign in Cartesian components of \ref PUCKERING with 6 membered rings (thanks to Carol Simoes and Javi Iglesias).
-- (users) LAMMPS patch has been finally removed. Notice that LAMMPS natively supports PLUMED now.
-- (users) AMBER patch has been finally removed. Notice that AMBER (sander module) natively supports PLUMED starting with version 15.
-- (developers) plumed can be compiled with arrayfire to enable for gpu code. \ref SAXS collective variable is available as part of the isdb module to provide an example of a gpu implementation for a CV