[gmx-users] Regarding PMF profile in umbrella samplling

[Sathish Kumar]

Yes it is positive charged....It has 48 + charges and RNA has 44 negative
charges.

On Fri, Jul 3, 2015 at 3:38 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

>
> > On 3 Jul 2015, at 11:31, Erik Marklund <erik.marklund at chem.ox.ac.uk>
> wrote:
> >
> > Hi,
> >
> > What is your pull geometry, and is your RNA periodic or somehow kept
> aligned with the x or z axes?
> >
>
> … and is your nanoparticle charged?
>
> Erik
>
> > Erik
> >
> > On 3 Jul 2015, at 09:50, Sathish Kumar <sathishk238 at gmail.com<mailto:
> sathishk238 at gmail.com>> wrote:
> >
> > Yes I have pulled upto 20 nm. The distance between final nanoparticle and
> > one end of the RNA is 48 nm. Total box size is 12 50 12. And there is no
> > periodic image interactions also. Please tell me what could be the reason
> > in this case.
> >
> > Thanks
> > sathish
> >
> > On Fri, Jul 3, 2015 at 1:30 AM, Sathish Kumar <sathishk238 at gmail.com
> <mailto:sathishk238 at gmail.com>> wrote:
> >
> > 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<mailto: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<mailto:
> 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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> > --
> > regards
> > M.SathishKumar
> >
> >
> >
> >
> > --
> > regards
> > M.SathishKumar
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-- 
regards
M.SathishKumar