I like to use tcl as my scripting language and after much pain and tribulation i have figured out how to get it to call gromacs without raising an error. Use exec -ignorestderr g_yourfavoritegromacsfunction. Note this will only work with versions of tcl 8.5 and later so if you use and older version (default if youre on ubuntu) and like using tcl than update it if you want to use it to call gromacs.
Jeremy
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