[gmx-users] Strange grompp error: System has non-zero total charge

[Suman Chakrabarty]

Hi,

I am trying energy minimization with a simple alkane chain in a DMSO
box. So there should not be any unbalanced charge on any individual
molecule. Each atom of the alkane is uncharged and DMSO has following
entries in dmso.itp file:

[ atoms ]
;   nr    type   resnr  residu  atom    cgnr    charge  mass
    1     SDMSO     1   DMSO    SDmso   1        0.139  32.06000
    2     CDMSO     1   DMSO    CDms1   1        0.16   15.03500
    3     ODMSO     1   DMSO    ODmso   1       -0.459  15.99940
    4     CDMSO     1   DMSO    CDms2   1        0.16   15.03500

So total charge on a DMSO is zero.

But when I run grompp for the energy minimization it complains:

NOTE 1 [file topol.top, line 548]:
  System has non-zero total charge: -4.882812e-04

The line 548 is the solvent entry in the topology file:

[ molecules ]
; Compound        #mols
Protein             1
DMSO                25948  ; line number 548


The note sometimes appears as error depending on some cut-off parameters
in the mdp file!

Now the question is that from where this (very small) non-zero total
charge of the system is coming, when individual molecules do not have
any charge? What would be the right way to rectify it?

Here is my mdp file for energy minimization:

title           = cg+steep energymin
cpp             = /lib/cpp

integrator      = cg
nsteps          = 3000
nstcgsteep      = 1000
comm_mode       = linear
nstcomm         = 1

emtol           = 1.0
emstep          = 0.01

nstxout         = 100
nstvout         = 100
nstfout         = 100
nstlog          = 100
nstenergy       = 100
energygrps      = protein DMSO

nstlist         = 5
ns_type         = grid
pbc             = xyz
rlist           = 1.2

coulombtype     = PME
rcoulomb        = 1.2

vdwtype         = cut-off
rvdw            = 1.2

fourier_spacing = 0.20
pme_order       = 6
ewald_rtol      = 1e-6
optimize_fft    = yes

constraints     = none



Thanks and regards,
Suman Chakrabarty.