[gmx-users] a program to calculate the adsorbed molecules

[Justin Lemkul]

On 5/7/13 2:04 PM, Za Pour wrote:
> Dear gmx users
> I would like to calculate the number of the surfactant molecules adsorbed on the
> nanotube surface as a function of time. I would be pleased if anyone could tell me
> whether there is a program in gromacs to do that or not?

Not directly, but perhaps you can integrate an RDF if designed cleverly. 
Otherwise, you'll have to script calls to g_dist or g_mindist with whatever 
adsorption criteria you have established for each molecule and count the frames 
in which the criteria are satisfied.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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