[gmx-users] CNT in water
abhijitchemiitd at gmail.com
Sat Jan 11 07:19:53 CET 2014
when you are creating the forcefield for cnt by g_x2top there you can
easily modify the sigma and epsilon value. For that you need to add some
values in ffnonbonden.itp file.
On Sat, Jan 11, 2014 at 7:07 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 1/10/14, 6:14 PM, Michelle Aranha wrote:
>> 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
>> 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
>> 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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