From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Mon May 23 2016 - 19:52:56 CDT
Dear Jeff,
Thankyou for providing the information. The download link is not working to download the tutorial files. I can only download the the pdf file.
Thanks and regards
Abhi
Abhishek Tyagi
PhD Student
Chemical and Biomolecular Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong
________________________________
From: Jeff Comer <jeffcomer_at_gmail.com>
Sent: Tuesday, May 24, 2016 1:02 AM
To: NAMD list; Abhishek TYAGI
Cc: Madhulika Gupta
Subject: Re: namd-l: Adsorption energy of protein in vacuum
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<mailto: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<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of Madhulika Gupta <gmadhulika1909_at_gmail.com<mailto: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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