sakthi kumaran wrote:
On Wed, Feb 23, 2011 at 5:25 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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
========================================
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