Re: Adsorption energy of protein in vacuum

From: Jeff Comer (
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:

We've also written a tutorial based on this:

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:


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

On Sun, May 22, 2016 at 10:46 PM, Abhishek TYAGI <>

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

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