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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
