[gmx-users] Adding metal ions near graphene sheet

[#SUKRITI GUPTA#]

Dear Gromacs users,

I want to simulate a system with graphene sheet with water around it containing some metal ions. I want these metal ions to be present very close to the graphene sheet. By using genbox or genion commands I can get ions to be inserted randomly in the system but not at the location I want them to be present. Can anyone please let me know if it is possible to get metal ions replace the water molecule from the region we want it to? I tried adding ion near the sheet by adding the ion in the graphene pdb file itself and also by firstly taking a small simulation box and adding ions using genbox and later expanding the box and filling it with water. But in both these cases, during energy minimization I get error that segmentation fault / core dumped.

Please let me know if anyone has an idea of how to do this.

Thanks and Regards
Sukriti




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Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
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