[gmx-users] Regarding PMF profile in umbrella samplling

[Sathish Kumar]

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> 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
> > 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
>> > --
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>
>
>
> --
> regards
> M.SathishKumar
>



-- 
regards
M.SathishKumar