Hi,

An .mdp file in gromacs uses the following syntax:

left-hand keyword = right-hand keyword(s)

The warning says that the "'cutoff-scheme" keyword is simply not known in version 4.5.6, as it just appeared in later versions. Note that this is a warning, and not an error. In newer versions, you have the option to select among more than one cut-off scheme; in 4.5.6, there was just one scheme.

HTH,

J R Rodrigues

Thank you so much. So i should ignore it by using -maxwarn 1. Right

No. Using maxwarn is a dangerous thing.

You are asking Gromacs 4.5.6 to use “cutoff-scheme   = Verlet”. Gromacs 4.5.6 is unable to use that scheme, because the Verlet scheme was introduced in version 4.6. So, you have two options:

- If you really want to use the Verlet scheme, use a newer Gromacs version;

- If you’re OK with using the traditional cut-off scheme, just delete that line in your .mdp file.

For more information, look at:

http://www.gromacs.org/Documentation/Cut-off_schemes

Got it. Thanks Joaquim for your text.

Hi Joaquim Rui Rodrigues, I'm currently using Gromacs 4.5.5. Does your suggestion apply for the following as well?

WARNING 1 [file md.mdp, line 50]:

Unknown left-hand 'nstxout-compressed' in parameter file

WARNING 2 [file md.mdp, line 50]:

Unknown left-hand 'compressed-x-grps' in parameter file

Shall I just delete these lines instead of using maxwarn?

Look forward to your answer at the earliest.

Yes, You can make comment of these two line, however you can make xtc after simulation using trr file.