[gmx-users] Fwd: Net charge error

Siddhesh Kamat canalesvcf09 at gmail.com
Sun Jan 11 16:57:21 CET 2015

Hello everyone,
Thanks for the prompt reply. I have attached the .itp and .top files of
MPNA(monoprotic napthenic acid). This is the error I get on energy
command line
gmx grompp -f minim.mdp -c MPNA_solv.gro -p topol.top -o em.tpr

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#

NOTE 1 [file minim.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.

Setting the LD random seed to 2203031122
Generated 331705 of the 331705 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 331705 of the 331705 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'MPNA'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 2 [file topol.top, line 20]:
  System has non-zero total charge: 452.808792
  Total charge should normally be an integer. See
  for discussion on how close it should be to an integer.

Program gmx, VERSION 5.0.2
Source code file:
/home/canales/gromacs-5.0.2/src/gromacs/gmxpreprocess/grompp.c, line: 603

Fatal error:
number of coordinates in coordinate file (MPNA_solv.gro, 4883)
             does not match topology (topol.top, 4884)

Siddhesh Kamat

More information about the gromacs.org_gmx-users mailing list