Hi gmx-users and gmx-developers, There are a number of features of GROMACS that we plan to drop for 5.0 (scheduled for early 2014). We don’t like doing this, but if things are broken or cause developers pain, then they will go unless there is manpower to support them. We’d like to keep you informed and hear how much pain any of this might cause. Some features will be dropped entirely, and others are likely to be reduced to explicit support only for some cases. Some discussion has already occurred here http://redmine.gromacs.org/issues/1292.
Things we plan to drop entirely: * particle decomposition (see below) * current QM support (this will be dropped, work on a replacement is underway, planned for 5.0) * writing of pair distance and/or time-averaged pair distance to energy files during simulations with position/orientation restraints * reaction-field-nec * Encad-shift * mdrun -ionize * GCT * mdrun -seppot * mdrun -ffscan * OpenMM support There are several algorithms (e.g. fancy kinds of restraints) that have only ever worked with particle decomposition (if they work at all...). We plan to support these only in serial. Things that will likely only work in serial (ie. single-domain DD): * ensemble- and time-averaged distance restraints * L-BFGS energy minimization * Generalized Born In some cases, “in serial” might mean “in parallel (with DD) with an extra communication stage that will make it work, but might scale poorly.” Or “in parallel but if things diffuse too far, the simulation will crash.” If you have working examples of any of the above in parallel, we would be most interested to hear from you. We’d like to construct test cases that show what works now, so that later if we are able to support some kind of parallelism, we can show that it still works. Things that won’t support constraints (because the implementations are broken or missing): * L-BFGS energy minimization * MTTK pressure coupling As always, what goes into GROMACS depends on people putting the work in. If something above would affect you, then do speak up. Contributions of working test cases are particularly valuable, but in the end you might have to be the one to write the code to make the test pass. You will have the option of continuing to use old code, too! Cheers, Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists