[gmx-users] adsoption of peptide into surface

[Justin Lemkul]

On 7/8/16 12:13 PM, Alexander Alexander wrote:
> Dear Gromacs user,
>
> I want to compare the adsorption behavior of four different short peptides
> into a solid surface in aqueous solution to indicate which one of them has
> stuck stronger on the solid surface and the driving force behind the
> adsorption as well.
>
> The 80 ns simulations of each of them have been already finished
> successfully.The "gmx distance and "gmx pairdist" helped me to see how the
> peptides are approaching the surface, but not surely enough to reach my
> goals, so, I would be so appreciated if you could suggest some parameters
> calculable(easier that PMF and FEP) in gromacs that address me to my goal.
>

To argue strength/affinity, you need an energetic argument.  PMF is 
straightforward and most appropriate here.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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