HI
I have a simulation box with 51.05x51.58x71 A.
base on stoichiometry calculation we need 5936 number of water molecules in this simulation box.
also, stoichiometry calculation show, for 0.71 molarity NaCl we must add 76 Na+ ions and 76 cl- Ions.
for add, these ions, how many water molecules must be deleted from the simulation box?
Hi Seyed,
You are doing that with gromacs, gmx genion wiil help you to replace the right number of water molecules. You must select water molecules when genion ask you which molecule you want to replace the ions with.
http://manual.gromacs.org/archive/5.0.4/programs/gmx-genion.html
As mentioned by Martiniano Bello , if you conduct your MD simulation using GROMACS (any versions), the water molecules will be replaced with necessary ions or counter ions (depending on your options).
Using Gromacs,
Please use gmx grompp comand first, it will calculate what are the amount of ions (how much positive or negative) you have to add to make your solution a neutral. Then use genion command with "-nname CL -nn 1 -conc 0.150 -neutral (if charges are positive), -pname NA -np 1 -conc 0.150 -neutral (if charges are negative)".
Then it will ask which molecules do you want to replace. Please choose "SOL". You don't have to calculate these things, Gromacs will automatically do this with grompp followed by genion commands.
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