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

[Tushar Ranjan Moharana]

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