[gmx-users] Regarding PMF profile in umbrella samplling
erik.marklund at chem.ox.ac.uk
Fri Jul 3 10:25:50 CEST 2015
Do you actually pull it 20 nm from the DNA, or is your plot showing the wrong units? If that is correct, you have very long-reaching effective interactions in your system. How big is your nanoparticle?
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
> On 3 Jul 2015, at 08:28, Sathish Kumar <sathishk238 at gmail.com> wrote:
> Dear gromacs-users,
> I have run umbrella samplling for RNA and
> nanoparticle. For this system, I got the PMF in which there is no plateau
> value and it has constant minimum value. in the last window of umbrella
> samplling, there is no interaction between RNA and nanoparticle and even
> though adding of more windows also I am not getting plateu value in PMF
> profile. From this profile can i calculate the binding free energy? please
> suggest me.
> The link for the PMF profile
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