[gmx-users] Applied electric field on the pure water

[Saeid Akbarshahi]

The simulation box contains just water molecules

** water.pdb **
ATOM     1   OW  SOL    1       19.350   2.371   0.000  0.00  0.00             
ATOM     2   HW1 SOL    1       18.600   2.951   0.000  0.00  0.00             
ATOM     3   HW2 SOL    1       20.100   2.951   0.000  0.00  0.00             
END
** md.mdp **
integrator= md
nsteps= 100000000 ; 200 ns
dt= 0.002; 2 fs
comm-mode                = Linear
ns_type= grid
nstlist= 5
rlist= 1
rcoulomb= 1
rvdw= 1
coulombtype= PME

pme_order= 4
fourierspacing= 0.15
ewald_rtol      = 1e-05
optimize_fft    = yes
tcoupl= V-rescale

tc-grps= System
tau_t= 0.1
ref_t= 300 
pbc= xyz
vdw-type        = Cut-off

gen_vel= no  
constraints              = all-bonds
DispCorr                 = Ener
constraint-algorithm     = Lincs
lincs-order              = 4
lincs-iter               = 1
lincs-warnangle          = 30
E-z                      = 1 0.000001 0 ;10 v/cm

---- Commands ----
pdb2gmx -f water.pdb -posrefc 0
Force Field : AMBER99SB-ILDN  - Water TIP3P
editconf -f conf.gro -bt cubic -box 5 5 5
genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top
grompp -f min.mdp -c 5.gro -p topol.top
mdrun -s topol.tpr
grompp -f md.mdp -c confout.gro -p topol.top -o md.tpr
mdrun -s md.tpr
1. Whether is correct simulation pure water ?
2.Chart potential.JPG (If request ، attach in next post) shows the electric field 0.003 v/nm !? whereas applied electric field 0.000001 v/nm in md.mdp.
Do I wrong in the applied electric field 1000 v/m ?
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