[gmx-users] two warnings in umbralla sampling step 6

sunyeping sunyeping at aliyun.com
Sat Oct 26 16:44:43 CEST 2013

Dear gromacs user,
I am doing umbralla sampling on a protein-ligand system following the gromacs umbralla sampling turial. It seems that the first five steps go well, and I select 23 gro files as the starting configurations of adjacent umbrella sampling windows. However when I use grompp to generate tpr files for these individual configurations as following: 
grompp -f npt_umbrella.mdp -c conf86.gro -p topol.top -n index.ndx -o npt86.tprI get the following notes, warning and error information:NOTE 1 [file npt_umbrella.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy
NOTE 2 [file npt_umbrella.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

WARNING 1 [file npt_umbrella.mdp]:
  You are generating velocities so I am assuming you are equilibrating a
  system. You are using Parrinello-Rahman pressure coupling, but this can
  be unstable for equilibration. If your system crashes, try equilibrating
  first with Berendsen pressure coupling. If you are not equilibrating the
  system, you can probably ignore this warning.
...............Largest charge group radii for Van der Waals: 16.306, 16.297 nm
Largest charge group radii for Coulomb:       16.306, 16.297 nm

WARNING 2 [file npt_umbrella.mdp]:
  The sum of the two largest charge group radii (32.603355) is larger than
  rlist (1.400000)
....................Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
Discussion aout warring 2 on the mail-list points out that the error that cause warning 2 will impact the results and lead to artifacts. I cann't understand why the warning occurs here, because it didn't appear when I use grompp in the my previous steps.  Could you explain why it occur in this step? Will it really affect umbralla sampling? Can I use the -maxwarn option to ignore it?
Best Regards,
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

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