mdp文件-GROMACS

2022年4月19日 
md-lywu.mdpmd-vsremd-lywu.mdp
NOTE 1 [file smd.mdp, line 46]:
  smd.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.
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
NOTE 2 [file smd.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy
  
  NOTE 3 [file topol.top, line 2238]:
  The bond in molecule-type MOL between atoms 7 C7 and 8 N1 has an
  estimated oscillational period of 1.8e-02 ps, which is less than 10 times
  the time step of 2.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.