[gmx-users] Regarding PMF profile in umbrella samplling

[Sathish Kumar]

Thank you for your kind reply.

I pull the RNA from one end of the strand away from nanoparticle.
Nanoparticle contains 200 atoms. The distance between center of mass of
nanoparticle and RNA in last window is 20 nm only.

Best
sathish

On Fri, Jul 3, 2015 at 1:25 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
regards
M.SathishKumar