[gmx-users] Re: applied electric field on the pure water

Saeid Akbarshahi saeidakbarshahi at yahoo.com
Thu Sep 29 09:08:33 CEST 2011

Dear users

The simulation box contains just water molecules

---- 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 170 ns.png (attach) shows the electric field 0.003 v/nm !? whereas applied electric field 0.000001 v/nm in md.mdp(attach).

Do I wrong in the applied electric field 1000 v/m ?
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