[gmx-users] Van der waals interaction between nanotubes

[Justin A. Lemkul]

sakthi kumaran wrote:
> 
> 
> On Wed, Feb 23, 2011 at 5:25 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     sakthi kumaran wrote:
> 
>         Dear all,
>                 Hi I am new to gromacs. I want to calculate the Van der
>         waals interaction between two capped CNT facing each other using
>         the pairwise LJ potential.I haven't used gromacs already. Any
>         know-how/procedures to do the requiste would be very
>         helpful.Whether Any tutorials are available for such a kind of
>         thing...
>          
> 
> 
>     Running a simulation while setting proper energygrps to decompose
>     short-range nonbonded interactions sounds to be what you need to do.
> 
>     -Justin
> 
> 
>          Thank you in advance guys
>          
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> _sorry I am not getting that. Please explain_

When you run the simulation, set the energygrps keyword in your .mdp file so 
that you have each of your groups of interest specified.  The nonbonded 
potential will be decomposed and the short-range LJ and Coulombic interactions 
are written to the .edr file pairwise for each group, i.e.:

energygrps = A B

will give you energy terms for A-A, A-B, and B-B interactions.

Beyond that, please consult basic tutorial material, the carbon nanotube how-to 
on the Gromacs site, and the extensive discussions of these systems in the list 
archive.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================