I wanted to simulate NaOH in water using MD. However there are some problems I have:
1- How to add hydroxide ions in a simulation box? Is there any other way than removing H from some of the water molecules? Is there any software for this?
2- After that how to set the force fields for NaOH? Can we use CHARMM or should we add the parameters ouselves? Because I used it and it gave me error.
I want to use LAMMPS for simulations.
Thanks in advance.
Dear Mohammad Shakiba,
(1) We can develop codes to create a document with the information of the simulation box (id, atoms positions, box length,...) in GNU Octave and then use the read_data command to import it in the simulation code. (2) it depends on the interatomic potential and the commands used to modify the simulation box. I recommend the LAMMPS manual.
https://lammps.sandia.gov/doc/commands_list.html
I hope that helps you.
Wilmer
Hydroxide ion should be parametrized in charmm (see https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/att-1417/toppar_water_ions.mod.str , there are OX-HX bond parameters for OH-). The topology should be trivial to construct; after that you can use VMD to add OH- ions in bulk.
Dear Bartosz Trzaskowski , Wilmer Velilla-Díaz , Zhaoxi Sun
Thank you all for your answers. I'm trying to test them...:))
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