[gmx-users] CNT in water

[abhijit Kayal]

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:
>
>> 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
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur