From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Mon May 23 2016 - 12:02:17 CDT
Dear Abhishek, Mudhulika,
If you're interested in doing free-energy calculations of adsorption from
water on graphene, you might want to have a look at our paper:
http://dx.doi.org/10.1021/acsnano.5b03592
We've also written a tutorial based on this:
http://jeffcomer.us/tutorials.html
It might be possible to use the same approach on other surfaces, but you
need to find a good force field. We've used a silver force field created by
the Walsh group: http://dx.doi.org/10.1021/acs.langmuir.5b03601
Jeff
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us
On Sun, May 22, 2016 at 10:46 PM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk>
wrote:
> Dear Madhulika,
>
>
> What kind of method you used for adsorption energy calculation. I would
> like to know, I am also working on surface adsorption of DNA on graphene.
> Can you please explain the method or protocol you used.
>
>
> I think you used SASA?
>
>
>
> Abhishek Tyagi
>
> PhD Student
>
> Chemical and Biomolecular Engineering
>
> Hong Kong University of Science and Technology
>
> Clear Water Bay, Hong Kong
>
>
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Madhulika Gupta <gmadhulika1909_at_gmail.com>
> *Sent:* Friday, May 20, 2016 7:01:05 PM
> *To:* namd-l
> *Subject:* namd-l: Adsorption energy of protein in vacuum
>
> Dear All,
> I am trying to study protein adsorption on metal surface in vacuum in
> NAMD. I am getting almost double the adsorption energies values as that in
> explicit water and DFT studies.
> I am not sure if there is a different method to treat electrostatics and
> van der Waal forces in vacuum. I am using PME off and a cutoff of 12 A for
> 45X45X45 A box.
> Please advise as to how should I modify the vacuum simulations to get
> better results in namd?
>
>
> Thanks and Regards
> Madhulika
>
> --
> Madhulika Gupta
> Research Scholar
> Department of Chemistry
> Indian Institute of Technology, Delhi
> New Delhi-110016
>
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