Re: Adsorption energy of protein in vacuum

From: Abhishek TYAGI (
Date: Sun May 22 2016 - 22:46:38 CDT

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: <> on behalf of Madhulika Gupta <>
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 Gupta
Research Scholar
Department of Chemistry
Indian Institute of Technology, Delhi
New Delhi-110016

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