[gmx-users] CNT in water

Michelle Aranha maranha at utk.edu
Sat Jan 11 00:15:17 CET 2014


I am trying to simulate a simple system of CNT in bulk water. 
The steps that I have completed are: 
1. Create a pdb file for CNT. 
2. Use editconf to convert to a gro file and define the length of the
simulation box, the pbc etc. 
3. Create a forcefield folder in my current working directory containing the
bonded, nonbonded parameters for CNT molecules. 
4. Generate the topology using g_x2top. 
5. Solvate the box using genbox. 

Before proceeding any further with the simulation , 
I would like to know if I I have to use any combination rules for Carbon
water interaction and modify my forcefield  file to include this new carbon
water interaction potential parameters or does Gromacs take care of it i.e
does it automatically update the itp file to include the CNT water
interaction while solvating the CNT? 


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