Re: Adsorption energy of protein in vacuum

From: Ana Celia Vila Verde (
Date: Sat May 21 2016 - 04:17:54 CDT

Dear Madhulika,

I don't think there's anything in principle wrong with your NAMD
simulations in vaccuum. It is to be expected that the adsorption energy
of a protein onto a surface in the absence of solvent should be very
different from that calculated in the presence of solvent (even when
using the same force field).

I hope this helps,


On 20/05/16 13:01, Madhulika Gupta wrote:
> 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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