[gmx-users] Regarding PMF profile in umbrella samplling

[Erik Marklund]

Dear Sathish,

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?

Kind regards,
Erik


Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

> 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
> 
> https://www.dropbox.com/s/xibm1f6oxx2d5hc/PMF238.png?dl=0
> 
> 
> Thanks
> Sathish
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