[gmx-users] NPT equilibration in KALP15-DPPC

[Shima Arasteh]

 Hi,

For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when I run the grompp command, I get 4 notes. Is it necessary to pay attention to the notes ? Are they notable?


NOTE 1 [file npt.mdp]:
  You are using a cut-off for VdW interactions with NVE, for good energy
  conservation use vdwtype = Shift (possibly with DispCorr)


NOTE 2 [file npt.mdp]:
  You are using a cut-off for electrostatics with NVE, for good energy
  conservation use coulombtype = PME-Switch or Reaction-Field-zero

Generated 837 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'CL'

NOTE 3 [file topol.top, line 929]:
  The bond in molecule-type Protein between atoms 4 N and 5 H has an
  estimated oscillational period of 1.0e-02 ps, which is less than 10 times
  the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group rest is 33897.00

NOTE 4 [file npt.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame         -1 time  100.000   
Using frame at t = 100 ps
Starting time for run is 0 ps
Largest charge group radii for Van der Waals: 0.239, 0.234 nm
Largest charge group radii for Coulomb:       0.239, 0.234 nm
This run will generate roughly 1 Mb of data

There were 4 notes

Thanks for your suggestions in advance.

Sincerely,
Shima