On Fri, Nov 30, 2018 at 10:28 AM LEBOLD, KATHRYN MARIE <[email protected]> wrote: > > Hi all - > > > I've been attempting to run IBI in VOTCA in conjunction with Gromacs in a two > different ways and have run into errors with both of them, so I would > appreciate some advice: > > > Attempt 1: Compiled VOTCA with Gromacs 2016.4 which was compiled with MPI and > double precision (the executable is therefore gmx_mpi_d). VOTCA doesn't seem > to be able to find this executable as it's looking for one called "gmx". Yeah, VOTCA is only looking for gmx and gmx_d, but you can tell CMake, which gmx executable to by setting GMX_EXECUTABLE as a CMake option, i.e. -DGMX_EXECUTABLE=/path/to/gmx_mpi_d GMX_EXECUTABLE changes the default value for all gmx invocations, i.e. also for gmx grompp. Alternatively you can set csg_get_property cg.inverse.gromacs.grompp.bin and cg.inverse.gromacs.mdrun.command in your xml setting file.
> Attempt 2: Compiled VOTCA with Gromacs 2018.4 which was compiled without MPI > for all executables except mdrun and in single precision, so there is a "gmx" > executable and an "mdrun_mpi" executable. When VOTCA runs, it calls "gmx > mdrun" rather than the parallelizable "mdrun_mpi," which works but doesn't > take advantage of the parallelization of Gromacs. Here you can change the default value by setting the cg.inverse.gromacs.mdrun.command option in your xml file. This will only overwrite the value for mdrun invocation, but not gmx invocation (e.g. for grompp) > > > So my question boils down to how to tell VOTCA what the Gromacs executables > it's using are named, and whether different names can be specified for > pre-processing (grompp) and actually running md simulations (mdrun). Yes, there are options for everything, have a look at the manual (http://doc.votca.org/manual.pdf) section 10.4 in the gromacs block. Christoph > > Thanks, > Kate > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
