diff --git a/src/colvar/CH3Shifts.cpp b/src/colvar/CH3Shifts.cpp index 7eb9a88e0872fa064d6ebcb64ad689ecdbbe9406..2ee90e8c74295941c7f0988c7b185f20c038b010 100644 --- a/src/colvar/CH3Shifts.cpp +++ b/src/colvar/CH3Shifts.cpp @@ -49,27 +49,12 @@ values to generate a score \cite Robustelli:2010dn \cite Granata:2013dk. It is also possible to backcalculate the chemical shifts from multiple replicas and then average them to perform Replica-Averaged Restrained MD simulations \cite Camilloni:2012je \cite Camilloni:2013hs. -HOW TO COMPILE IT - In general the system for which chemical shifts are to be calculated must be completly included in -ATOMS. It should also be made WHOLE before the the backcalculation. CH3Shift is included in the -free package ALMOST v.2.1 that can be dowload via SVN (svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code). -ALMOST 2.1 can be found in branches/almost-2.1/ and it can be compiled: - -\verbatim -./configure -make -\endverbatim +ATOMS. It should also be made whole \ref WHOLEMOLECULES before the the back-calculation. -Once the code is compiled you should see the ALMOST library libAlm.a in src/lib/ - -PLUMED 2 must then be compiled with ALMOST enabled: - -\verbatim -./configure --enable-almost CPPFLAGS="-I/ALMOST_BASE_PATH/branches/almost-2.1/include -I/ALMOST_BASE_PATH/branches/almost-2.1/include/almost -I/ALMOST_BASE_PATH/branches/almost-2.1/lib/sqlite-3.6.23.1" LDFLAGS="-L/ALMOST_BASE_PATH/branches/almost-2.1/src/lib -lAlm -L/ALMOST_BASE_PATH/branches/almost-2.1/lib/sqlite-3.6.23.1 -lsqlite3 -lz -lbz2 -L/ALMOST_BASE_PATH/branches/almost-2.1/src/forcefield -lnbimpl -L/ALMOST_BASE_PATH/branches/almost-2.1/src/lib/modules -lshx" +HOW TO COMPILE IT -with ALMOST_BASE_PATH the full path to the ALMOST folder -\endverbatim +\ref installingalmost on how to compile PLUMED with ALMOST. HOW TO USE IT diff --git a/src/colvar/CS2Backbone.cpp b/src/colvar/CS2Backbone.cpp index f1367284cf78f8cda67fed0dbb16fe8b7aab3d78..637488514d351c3f6e5f414cf4f0cefbad5a4881 100644 --- a/src/colvar/CS2Backbone.cpp +++ b/src/colvar/CS2Backbone.cpp @@ -44,30 +44,15 @@ experimental backbone chemical shifts for a protein (CA, CB, C', H, HA, N). CamShift \cite Kohlhoff:2009us is employed to back calculate the chemical shifts that are then compared with a set of experimental values to generate a score \cite Robustelli:2010dn \cite Granata:2013dk. -It is also possible to backcalculate the chemical shifts from multiple replicas and then average them +It is also possible to back-calculate the chemical shifts from multiple replicas and then average them to perform Replica-Averaged Restrained MD simulations \cite Camilloni:2012je \cite Camilloni:2013hs. -HOW TO COMPILE IT - In general the system for which chemical shifts are to be calculated must be completly included in -ATOMS. It should also be made WHOLE before the the backcalculation. CamShift is included in the -free package ALMOST v.2.1 that can be dowloaded via SVN (svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code). -ALMOST 2.1 can be found in branches/almost-2.1/ and it can be compiled: - -\verbatim -./configure -make -\endverbatim +ATOMS. It should also be made whole \ref WHOLEMOLECULES before the the back-calculation. -Once the code is compiled you should see the ALMOST library libAlm.a in src/lib/ - -PLUMED 2 must then be configured with ALMOST enabled: - -\verbatim -./configure --enable-almost CPPFLAGS="-I/ALMOST_BASE_PATH/branches/almost-2.1/include -I/ALMOST_BASE_PATH/branches/almost-2.1/include/almost -I/ALMOST_BASE_PATH/branches/almost-2.1/lib/sqlite-3.6.23.1" LDFLAGS="-L/ALMOST_BASE_PATH/branches/almost-2.1/src/lib -lAlm -L/ALMOST_BASE_PATH/branches/almost-2.1/lib/sqlite-3.6.23.1 -lsqlite3 -lz -lbz2 -L/ALMOST_BASE_PATH/branches/almost-2.1/src/forcefield -lnbimpl -L/ALMOST_BASE_PATH/branches/almost-2.1/src/lib/modules -lshx" +HOW TO COMPILE IT -with ALMOST_BASE_PATH the full path to the ALMOST folder -\endverbatim +\ref installingalmost on how to compile PLUMED with ALMOST. HOW TO USE IT diff --git a/user-doc/Installation.txt b/user-doc/Installation.txt index 8d20748acfb835c3b08e801645d66df842782853..ef5a5bf5ce02a02e4f0704a02d15fbdb85defc88 100644 --- a/user-doc/Installation.txt +++ b/user-doc/Installation.txt @@ -378,5 +378,29 @@ it. Refer to the <a href="../../developer-doc/html/index.html"> developer manual </a>. +\section installingalmost Installing PLUMED with ALMOST + +In order to used some of the NMR based collective variables (\ref CS2BACKBONE and \ref CH3SHIFTS) PLUMED needs to be linked with ALMOST. + +The free package ALMOST v.2.1 that MUST be dowloaded via SVN (svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code). +ALMOST 2.1 can be found in branches/almost-2.1/ and it can be compiled: + +\warning ALMOST needs SQLITE3, GZIP and BZIP2 installed on your computer. + +\verbatim +./configure --prefix="wherever you want it" +make +make install +\endverbatim + +PLUMED will not use the RDCs module of ALMOST so you can ignore the warning about the LAPACK. + +Once ALMOST is installeed, PLUMED 2 can then be configured with ALMOST enabled: + +\verbatim +./configure --enable-almost CPPFLAGS="-I/ALMOST_INSTALL_PATH/include -I/ALMOST_INSTALL_PATH/include/almost" LDFLAGS="-L/ALMOST_INSTALL_PATH/lib" +\endverbatim +with ALMOST_INSTALL_PATH the full path to the ALMOST installation folder. + */