diff --git a/patches/gromacs-4.6.7.config b/patches/gromacs-4.6.7.config index 6282d3f77a44f28a8ecfc14161ebfe814b5c3699..678f137f409f1fa4aa489554c57221f7ee2dd932 100644 --- a/patches/gromacs-4.6.7.config +++ b/patches/gromacs-4.6.7.config @@ -16,24 +16,9 @@ specify the name of the PLUMED input file, e.g.: mdrun -plumed plumed.dat -For more information on gromacs you should visit http://www.gromacs.org - -This is an experimental patch to perform Hamiltonian replica exchange with GROMACS -Implementation described in: - Bussi, Hamiltonian replica-exchange in GROMACS: a flexible implementation, - Mol. Phys., DOI: 10.1080/00268976.2013.824126 (2013) - -To use it: -* Prepare separate topologies (topol0.tpr, topol1.tpr, etc) -* Run a normal replica exchange with gromacs adding the flag "-hrex" on the command line +This patch also implements the -hrex keyword for gromacs. See \ref hrex -Suggested checks: -* Try with several identical force fields and different seed/starting point - Acceptance should be 1.0 - -Warnings: -* Topologies should have the same number of atoms, same masses and same constraint topology -* Choose neighbor list update that divides replex +For more information on gromacs you should visit http://www.gromacs.org EOF } diff --git a/patches/gromacs-5.1.2.config b/patches/gromacs-5.1.2.config index 430d161e4cc525b5e037b2eb1ebe7aabd080ed25..97adeda473c03a4d2d6305ec2532afda8bc5fa59 100644 --- a/patches/gromacs-5.1.2.config +++ b/patches/gromacs-5.1.2.config @@ -16,27 +16,9 @@ specify the name of the PLUMED input file, e.g.: gmx mdrun -plumed plumed.dat -For more information on gromacs you should visit http://www.gromacs.org - -This is an experimental patch to perform Hamiltonian replica exchange with GROMACS -Implementation described in: - Bussi, Hamiltonian replica-exchange in GROMACS: a flexible implementation, - Mol. Phys., DOI: 10.1080/00268976.2013.824126 (2013) - -To use it: -* Prepare separate topologies (topol0.tpr, topol1.tpr, etc) -* Run a normal replica exchange with gromacs adding the flag "-hrex" on the command line +This patch also implements the -hrex keyword for gromacs. See \ref hrex -Suggested checks: -* Try with several identical force fields and different seed/starting point - Acceptance should be 1.0 - -Warnings: -* Topologies should have the same number of atoms, same masses and same constraint topology -* Choose neighbor list update that divides replex - -EXTRA WARNING: THIS PATCH FOR GMX 5.1.2 IS STILL UNDER DEVELOPMENT - +For more information on gromacs you should visit http://www.gromacs.org EOF } diff --git a/user-doc/tutorials/hrex.txt b/user-doc/tutorials/hrex.txt index 4192adb379dc0a119b3ce07b56ef1e0071e246c7..4e18296e7a49b27498d2fef2d5b1e7ad24ceca82 100644 --- a/user-doc/tutorials/hrex.txt +++ b/user-doc/tutorials/hrex.txt @@ -1,16 +1,26 @@ /** \page hrex Using Hamiltonian replica exchange with GROMACS -If you patch GROMACS using this special PLUMED branch you should be able to perform -Hamiltonian replica exchange with different topologies. This patch is modifying GROMACS -much more than the original PLUMED patch, so: be even more careful! +When patching GROMACS with PLUMED, it is also possible to perform +Hamiltonian replica exchange with different topologies. +Although this feature is provided together with PLUMED, it is actually +a new feature for GROMACS itself that can be enabled using the `-hrex` +flag of `mdrun`. This implementation is very close to the one used to produce the data in this paper -\cite bussi2013mp. +\cite bussi2013mp. In case you find it useful, please cite this paper. + +\warning This feature is currently used by several groups and should be +robust enough. However, be sure that you understand its limitations and +to perform all the tests discussed in this page before using it in production. \section multipletopologies Generate multiple topologies -Use the plumed partial_tempering command line tool. +Plumed comes with a `partial_tempering` command line tool that can be used to generate +multiple topologies. Notice that you might want to generate these topologies +by userself. This step is totally independent from the use of the `-hrex` flag. + +The `partial_tempering` tool can be invoked as follows: \verbatim plumed partial_tempering scale < processed.top \endverbatim @@ -72,11 +82,11 @@ all other terms (bonds/bends) are identical. \section hrexpatch Run GROMACS -If GROMACS has been patched with this version of PLUMED it should accept the -hrex option -in mdrun. Please double check this (mdrun -h should list this possibility). Also -notice that only the patch for gromacs 4.6.5 implementes hrex. +If GROMACS has been patched with PLUMED it should accept the -hrex option +in mdrun. Please double check this (mdrun -h should list this possibility). +Notice that not all the versions of GROMACS allow this feature. First of all prepare separate topologies for each replicas using plumed partial_tempering -tool as shown above. Then run a normal replica exchange with gromacs adding the flag "-hrex" on the command line. +tool as shown above (or using some other tool). Then run a normal replica exchange with gromacs adding the flag "-hrex" on the command line. A complete run script could be adapted from the following \verbatim