[gmx-users] Regarding PMF profile in umbrella samplling

[Sathish Kumar]

Pull geometry = distance,
Pull rate = 0.005 nm/ps
RNA is aligned along Z-axis. it is not periodic.



On Fri, Jul 3, 2015 at 3:31 AM, 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?
>
> 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