Hi
I want to simulate graphene sheet in salt water. I am confused about adding salt content to the water box. Is it simply about adding molecules of NaCl or should we include it like Na+ and Cl- ? On the other hand should we replace the water molecules or we can simple add molecules into box?
Thank you.
Hello Rahul Suresh ,
Regarding LAMMPS, I can suggest you Moltemplate, where you can create your simulation box as you desired and use it for your LAMMPS simulation. As far as I understood, you are not exceeding the saturation point for the saltwater, so you can directly insert the Na+ and Cl- ions rather than the NaCl molecule itself.
In the "Water mixed with sodium & chloride ions" section below in the website (http://moltemplate.org/visual_examples.html), there is an example that is similar to yours. For the graphene sheet, I guess you can easily create it by just checking the other example scripts. Lastly, if you consider taking the example script for your simulation box, please make sure that your forcefield type and the parameters are valid.
Regards
Hi Rahul Suresh and Ahmet Burak Yıldırım,
I was wondering if when you added Na+ and Cl- if you ever encountered the error: 'No more replaceable solvent!'. I am wondering why I have this issue when adding concentrations above 1M. Thanks in advance, I greatly appreciate any advice you may have.
Hello Kaitlyn Swayze,
I am not familiar with Gromacs, however, I can suggest you to check whether you are close to the saturation point or not. You may try to add NaCl molecule itself, rather than the individual ions.
Also, it might be related to the size of the simulation box, where you may try to increase the size and the number of molecules, and then check if it helps.
Regards
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