[gmx-users] umbrella sampling error

[Nikhil Maroli]

Dear all,
im running umbrella sampling when invoke the following command i got the
follwoing warnings and grompp terminated becasue of so much warning
,initially i neutralised the My protein-Ligand system with NACl,so how come
there will be a charge?  (NOTE 5)what i can do for that?  can i use maxwarn
option as im running equilibration?

  gmx grompp -f npt_umbrella.mdp -c conf128.gro -p topol.top -n index.ndx
-o npt125.tpr


NOTE 1 [file npt_umbrella.mdp, line 66]:
  npt_umbrella.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 npt_umbrella.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.



NOTE 3 [file npt_umbrella.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


NOTE 4 [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.





*NOTE 5 [file topol.top, line 77254]:*
*  System has non-zero total charge: -11.999994*
*  Total charge should normally be an integer. See*
*  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
<http://www.gromacs.org/Documentation/Floating_Point_Arithmetic>*
*  for discussion on how close it should be to an integer.*




Setting gen_seed to 2839808349
Velocities were taken from a Maxwell distribution at 310 K
Removing all charge groups because cutoff-scheme=Verlet
Pull group 1 'Chain_A' has 8120 atoms
Pull group 2 'Chain_B' has 33 atoms
Number of degrees of freedom in T-Coupling group Protein is 16109.61
Number of degrees of freedom in T-Coupling group non-Protein is 108398.39
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 1.408 nm, buffer size 0.008 nm
Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x56x104, spacing 0.111 0.116 0.116
Pull group  natoms  pbc atom  distance at start  reference at t=0
       1      8120      4060
       2        33      8137       1.117 nm          1.117 nm
Estimate for the relative computational load of the PME mesh part: 0.10
This run will generate roughly 32 Mb of data

There were 5 notes

There was 1 warning

-------------------------------------------------------
Program gmx grompp, VERSION 5.1
Source code file:
/home/user/gromacs-5.1/src/gromacs/gmxpreprocess/grompp.c, line: 2107

Fatal error:
Too many warnings (1), gmx terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


-- 
Ragards,
Nikhil Maroli