[gmx-users] genion doesn't work in 4.6.1?

Albert mailmd2011 at gmail.com
Fri Apr 5 21:05:47 CEST 2013


  I found that there would be some problem of genion in 4.6.1:

grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr

NOTE 1 [file complex.top, line 44008]:
   System has non-zero total charge: -11.000000
   Total charge should normally be an integer. See
   for discussion on how close it should be to an integer.

genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom

Reading file ions.tpr, VERSION 4.6.1 (single precision)
Using a coulomb cut-off of 1.2 nm
No ions to add and no potential to calculate.

Obviously, the total charge of the system is -11.0, but genion doesn't 
add anything to netural it....

thank you very much

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