[gmx-users] Adsorption and nucleation of proteins on surfaces

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 24 14:32:20 CEST 2009

Agnese Zicari wrote:
> Dear all I am mainly a scientist and I would like to complete my 
> experimental data with some software simulation.
> Can Gromacs or model the adsorption and the nucleation of proteins on 
> surfaces or there is no technical feasibility for this Software on 
> such a modeling?

Theoretically, anything *could* be done with a simulation.  However, it may be 
very difficult to derive appropriate parameters that are self-consistent with 
protein force fields.  This is not a trivial task for anyone, especially someone 
starting out in simulations.

Gromacs is well-suited to the task, but you have to consider whether or not it 
would be worth the time (it could take months) it would take to develop the 
appropriate force field parameters for your surfaces.


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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