[gmx-users] Adding metal ions near graphene sheet

#SUKRITI GUPTA# SUKRITI002 at e.ntu.edu.sg
Tue Aug 26 06:29:35 CEST 2014

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 Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>

More information about the gromacs.org_gmx-users mailing list