[gmx-users] CNT in water

Justin Lemkul jalemkul at vt.edu
Sat Jan 11 02:39:21 CET 2014

On 1/10/14, 6:14 PM, Michelle Aranha wrote:
> Hi,
> 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?

Gromacs does whatever the [defaults] directive of the topology tells it.  If 
you're co-opting some existing force field to do this work, then that should 
already exist.  If you're creating the force field from scratch, you will need 
to tell it all kinds of things, including which type of combination rules are 
applied.  See Chapter 5 of the manual.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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