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I've tried to install gromacs on my system (10.11.5) via homebrew. The command I used was brew install gromacs and it appears to have worked fine; gromacs is in my usr/bin/Cellar, and shows up when I run brew list.

But, when I try to actually run any gromacs command, I just get a command not found error. When I try to run man gromacs it tells me there is no manual entry for gromacs; I get man entries as normal for other brew packages I'm using.

brew doctor output is pasted below, but nothing in there means anything to me. I'd appreciate your perspectives on how to make this work, or on what other information I might need to include.

I wonder if I need to modify my PATH, but if so I don't know how to do that or what to modify it to.

Cheers

brew doctor output after this Warning: Unbrewed dylibs were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected dylibs: /usr/local/lib/libtcl8.6.dylib /usr/local/lib/libtk8.6.dylib

Warning: Unbrewed header files were found in /usr/local/include. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected header files: /usr/local/include/fakemysql.h /usr/local/include/fakepq.h /usr/local/include/fakesql.h /usr/local/include/itcl.h /usr/local/include/itcl2TclOO.h /usr/local/include/itclDecls.h /usr/local/include/itclInt.h /usr/local/include/itclIntDecls.h /usr/local/include/itclMigrate2TclCore.h /usr/local/include/itclTclIntStubsFcn.h /usr/local/include/mysqlStubs.h /usr/local/include/odbcStubs.h /usr/local/include/pqStubs.h /usr/local/include/tcl.h /usr/local/include/tclDecls.h /usr/local/include/tclOO.h /usr/local/include/tclOODecls.h /usr/local/include/tclPlatDecls.h /usr/local/include/tclThread.h /usr/local/include/tclTomMath.h /usr/local/include/tclTomMathDecls.h /usr/local/include/tdbc.h /usr/local/include/tdbcDecls.h /usr/local/include/tdbcInt.h /usr/local/include/tk.h /usr/local/include/tkDecls.h /usr/local/include/tkPlatDecls.h

Warning: Unbrewed .la files were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected .la files: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f_threads.la

Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected .pc files: /usr/local/lib/pkgconfig/tcl.pc /usr/local/lib/pkgconfig/tk.pc

Warning: Unbrewed static libraries were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected static libraries: /usr/local/lib/libtclstub8.6.a /usr/local/lib/libtkstub8.6.a

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I figured it out myself, so I'm posting the answer in case anyone else has this problem.

The answer was that gromacs has changed since the version I used most recently, and the commands I was used to no longer exist. For example, the g_energy command now runs as gmx energy.

If you are also having this problem, gmx help commands should give you a list of what the commands are now.

Thanks for reading this!

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