[gmx-users] ions coupl to protein in .top

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 7 13:23:03 CET 2007

Yang Ye wrote:
> Instead of correcting .top file, this error relates to index file. You
> shall append the Ca ions to the SOL group for T-coupling.
> # make_ndx -f your.gro
> In the list printed, you shall see a SOL group and a Ca group adjacent
> to each other.
> Type "q" to quit and write the index file.
> # vi index.ndx # or your favorite text editor
> Find the Ca group by string "[ Ca ]", then remove the the line [ Ca ].
> In your grompp command line, append an option -n

This will work too, but the solution I suggest using Protein and
Non-Protein in your .mdp file is more general and less fiddly, and
you'll never have to do it twice for the same system when you change
some detail of the solvent.


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