[gmx-users] doubt about "Ignoring obsolete mdp entry"

[Mark Abraham]

Hi,

If you're trying to use such features, then you want to find out how they
are currently implemented and use those instead. Probably you don't care
about most of them. The defaults are all reasonably sensible, and if there
was some issue that you had to act upon, then you'd get an error or a
warning, rather than a note.

Mark

On Mon, Apr 18, 2016 at 5:34 PM Tushar Ranjan Moharana <
tusharranjanmoharana at gmail.com> wrote:

> Hi all,
> To calculate delta G of mutation I was following the following tutorial
>
> http://www3.mpibpc.mpg.de/groups/de_groot/cecam2015/peptide_mutation/
>
> However following outputs of grompp is confusing me
>
> Ignoring obsolete mdp entry 'cpp'
> Ignoring obsolete mdp entry 'domain-decomposition'
> Ignoring obsolete mdp entry 'andersen_seed'
> Ignoring obsolete mdp entry 'dihre'
> Ignoring obsolete mdp entry 'dihre-fc'
> Ignoring obsolete mdp entry 'dihre-tau'
> Ignoring obsolete mdp entry 'nstdihreout'
> Ignoring obsolete mdp entry 'nstcheckpoint'
> Ignoring obsolete mdp entry 'optimize_fft'
> Replacing old mdp entry 'unconstrained_start' by 'continuation'
> Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
> Replacing old mdp entry 'xtc_precision' by 'compressed-x-precision'
>
> I understand the last 3 line. I will be grateful if someone help me
> understand the first 9 line. There was also notes which I could understand.
>
> NOTE 1 [file md.mdp, line 235]:
>   md.mdp did not specify a value for the .mdp option "cutoff-scheme".
>   Probably it was first intended for use with GROMACS before 4.6. In 4.6,
>   the Verlet scheme was introduced, but the group scheme was still the
>   default. The default is now the Verlet scheme, so you will observe
>   different behaviour.
>
> NOTE 2 [file md.mdp]:
>   Setting nstcalcenergy (100) equal to nstdhdl (50)
>
> NOTE 3 [file md.mdp]:
>   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>   nstcomm to nstcalcenergy
>
>
> Thanks a lot for the help.
>
>
> "A society with free knowledge is better than a society with free food"
>
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
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