[gmx-users] new atom type and force field

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 27 00:32:16 CET 2009

Shuangxing Dai wrote:
> Hi, all gmx users:
>     I am doing a simulation with NaCl (and ZnO, GaN). I start with the 
> .pdb file. But the Gromacs cannot recognize my new atom, such as Na, Cl. 
> How to add new atoms to Gromacs?
>      I am going to use periodical boundary conditions and LJ potential, 
> shell model , apply loading , and check polarization. I do not know how 
> to set the force field for LJ potential. Anyone know this can help me ? 

You need to start with a thorough understanding of chapter 5 of the manual.


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