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 (attach) 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 ?
<<attachment: potential.JPG>>
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