[gmx-users] Regarding PMF profile in umbrella samplling

[Erik Marklund]

> 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
> 
> 
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> 
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