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

Justin Lemkul jalemkul at vt.edu
Tue May 7 20:24:00 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list