[gmx-users] Problem running simulation on gromacs 2018.8 version

[pooja kesari]

Dear All,

I m trying to do a protein-ligand simulation,
I am using GROMOS 43a force field, I have typed by protein and got the
ligand file from PRODRG.
I prepared the complex and added solvent. *The protein has -8.0 charge by
when i m neutralizing it only adds 7 positive charge.*



* 3328         OM    336    VAL     O1   1492     -0.635    15.9994   ;
qtot -7.365  3329         OM    336    VAL     O2   1492     -0.635
 15.9994   ; qtot -8*


When i added 8 positive charge using  the below command
gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL
-np 8







*[ molecules ]; Compound        #molsProtein_chain_B     11IN
  1SOL         22473NA               8*

Again in the minimization step it is showing a list of
*errors and warnings. *
NOTE 1 [file em.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 787146813
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
Excluding 3 bonded neighbours molecule type '1IN'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'

NOTE 2 [file topol.top, line 21027]:

*System has non-zero total charge: 1.000000  Total charge should normally
be an integer. *See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

WARNING 1 [file topol.top, line 21027]:
  *You are using Ewald electrostatics in a system with net charge*. This can
  lead to severe artifacts, such as ions moving into regions with low
  dielectric, due to the uniform background charge. We suggest to
  neutralize your system with counter ions, possibly in combination with a
  physiological salt concentration.

Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   335    Protein residues
There are:     1      Other residues
There are: 22473      Water residues
There are:     8        Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 145023.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x80x80, spacing 0.113 0.113 0.113
Estimate for the relative computational load of the PME mesh part: 0.20
This run will generate roughly 6 Mb of data

There were 2 notes

There was 1 warning
Please suggests how can overcome these errors.