[gmx-users] Regarding neutralization of lipid bilayer

[naga raju]

Dear gmx users,
                 
        I built POPE+POPG (total 128 lipid molecules)
lipid bilayer in 3:1 ratio. POPE has neutral charge
and POPG has one unit of negative charge.To this lipid
molecules 3941 water molecules are added.
While creating bilayer.tpr file, it is giving non-zero
total charge: -4.534399e+01 related information was
shown below.              
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Generated 1369 of the 2211 non-bonded parameter
combinations
Excluding 3 bonded neighbours for POPE 96
turning all bonds into constraints...
Excluding 3 bonded neighbours for DPOP 32
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 3941
turning all bonds into constraints...
NOTE:
  System has non-zero total charge: -4.534399e+01
 
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at
303 K
renumbering atomtypes...
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

To neutralize the lipid molecule, I used the fallowing
command:
genion -s bilayer.tpr -o bilayer-ions.pdb -np 45
-pname Na -pq 1
 
then it is showing as System has non-zero total
charge: -3.439894e-01 related information was shown
below
zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
processing topology...
Generated 1369 of the 2211 non-bonded parameter
combinations
Excluding 3 bonded neighbours for POPE 96
turning all bonds into constraints...
Excluding 3 bonded neighbours for DPOP 32
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 3896
turning all bonds into constraints...
Excluding 1 bonded neighbours for Na 45
turning all bonds into constraints...
NOTE:
  System has non-zero total charge: -3.439894e-01
 
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at
303 K
zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz

My question:
              System has only 32 negatively charged
molecules, so total charge must be 32 units. But it is
showing as  System has non-zero total charge:
-4.534399e+01, why it is showing 13 units more
negative.

        Any suggestions is appreciated.
                 Thank you in advance.

                                with best regards,
                                   Nagarju 
               



       
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