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
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
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
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
sathishk...@gmail.commailto:sathishk...@gmail.com wrote:
Yes I have pulled upto 20 nm. The distance between final nanoparticle and
one end of the
On 3 Jul 2015, at 11:31, Erik Marklund erik.markl...@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
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.markl...@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
Yes it is positive chargedIt has 48 + charges and RNA has 44 negative
charges.
On Fri, Jul 3, 2015 at 3:38 AM, Erik Marklund erik.markl...@chem.ox.ac.uk
wrote:
On 3 Jul 2015, at 11:31, Erik Marklund erik.markl...@chem.ox.ac.uk
wrote:
Hi,
What is your pull geometry, and is your
