[gmx-users] Regarding PMF profile in umbrella samplling

[Erik Marklund]

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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