From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Sun May 22 2016 - 22:46:38 CDT
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?
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
Subject: namd-l: Adsorption energy of protein in vacuum
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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